DXR DE Analysis

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Last updated: 2025-07-10

Checks: 6 1

Knit directory: Recovery_5FU/

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C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/new/counts_raw_matrix_EMP_250514.csv	data/new/counts_raw_matrix_EMP_250514.csv

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/figure/
    Ignored:    data/Anat HM/
    Ignored:    data/CDKN1A_geneplot_Dox.RDS
    Ignored:    data/Cormotif_dox.RDS
    Ignored:    data/Cormotif_prob_gene_list.RDS
    Ignored:    data/Cormotif_prob_gene_list_doxonly.RDS
    Ignored:    data/DMSO_TNN13_plot.RDS
    Ignored:    data/DOX_TNN13_plot.RDS
    Ignored:    data/DOXgeneplots.RDS
    Ignored:    data/ExpressionMatrix_EMP.csv
    Ignored:    data/Ind1_DOX_Spearman_plot.RDS
    Ignored:    data/Ind6REP_Spearman_list.csv
    Ignored:    data/Ind6REP_Spearman_plot.RDS
    Ignored:    data/Ind6REP_Spearman_set.csv
    Ignored:    data/Ind6_Spearman_plot.RDS
    Ignored:    data/MDM2_geneplot_Dox.RDS
    Ignored:    data/Metadata.csv
    Ignored:    data/SIRT1_geneplot_Dox.RDS
    Ignored:    data/Sample_annotated.csv
    Ignored:    data/SpearmanHeatmapMatrix_EMP
    Ignored:    data/VennDiagram_DEGs.csv.2025-05-19_13-04-29.204911.log
    Ignored:    data/VolcanoPlot_D144R_original_EMP_250623.png
    Ignored:    data/VolcanoPlot_D24R_original_EMP_250623.png
    Ignored:    data/VolcanoPlot_D24T_original_EMP_250623.png
    Ignored:    data/annot_dox.RDS
    Ignored:    data/annot_list_hm.csv
    Ignored:    data/cormotifARclust_pp.RDS
    Ignored:    data/cormotif_dxr_1.RDS
    Ignored:    data/cormotif_dxr_2.RDS
    Ignored:    data/counts/
    Ignored:    data/counts_DE_df_dox.RDS
    Ignored:    data/counts_DE_raw_data.RDS
    Ignored:    data/counts_raw_filt.RDS
    Ignored:    data/counts_raw_matrix.RDS
    Ignored:    data/counts_raw_matrix_EMP_250514.csv
    Ignored:    data/d24_Spearman_plot.RDS
    Ignored:    data/dge_calc_dxr.RDS
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    Ignored:    data/ensembl_backup_dox.RDS
    Ignored:    data/fC_AllCounts.RDS
    Ignored:    data/fC_DOXCounts.RDS
    Ignored:    data/featureCounts_Concat_Matrix_DOXSamples_EMP_250430.csv
    Ignored:    data/filcpm_colnames_matrix.csv
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    Ignored:    data/gene_clustlike_motif.RDS
    Ignored:    data/gene_postprob_motif.RDS
    Ignored:    data/genedf_dxr.RDS
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    Ignored:    data/heartgenes.csv
    Ignored:    data/heartgenes_dox.csv
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/DXR_Project_Analysis.Rmd) and HTML (docs/DXR_Project_Analysis.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	73c8641	emmapfort	2025-07-10	Updated Analysis 07/10/25 EMP
html	54b2620	emmapfort	2025-07-08	Build site.
Rmd	425d3aa	emmapfort	2025-07-08	Updated Analysis 07/08/25
Rmd	a43fb2c	emmapfort	2025-07-07	Updated Analysis 07/07/25 EMP Proportion Barplots Cormotif p53, DDR, DIC gene sets
html	1b8f045	emmapfort	2025-07-03	Build site.
Rmd	10b885f	emmapfort	2025-07-03	Updated Website 07/03/25 EMP
html	14cdab3	emmapfort	2025-07-02	Build site.
Rmd	abdf4fe	emmapfort	2025-07-02	Updated Website with Streamlined Analysis 07/02/25 EMP
html	0b1ffad	emmapfort	2025-07-02	Build site.
Rmd	35bbd4f	emmapfort	2025-07-02	Updated Analysis all in one place EMP - 07/02/25
Rmd	81e180f	emmapfort	2025-06-27	RUVs Cormotif + updated analysis 06/27/25
Rmd	82c6704	emmapfort	2025-06-23	Updated Analysis 06/23/25
Rmd	98a546f	emmapfort	2025-06-16	06/16/25
Rmd	f530175	emmapfort	2025-06-16	Updating Analysis 06/16/25
Rmd	9f609f6	emmapfort	2025-06-13	Update 06/13/25
html	1d4d1de	emmapfort	2025-05-16	Build site.
html	29a5c35	emmapfort	2025-05-16	Build site.
Rmd	5db2858	emmapfort	2025-05-16	Removing copied pages + including final analysis
Rmd	b6f4e9c	emmapfort	2025-05-16	Updated Analysis 05/15/25
Rmd	32de50d	emmapfort	2025-05-14	Analysis Overhaul 05/14/25

---

editor_options: chunk_output_type: inline

I did this part with Sayan according to his analysis to ensure that my matrix was consistent with his - allowing me to work on downstream analysis #Read in Libraries

#Read in Counts Files from FeatureCounts

#load in libraries needed
#these counts files are from featureCounts, all saved as RDS objects

# ####Individual 1 - 84-1####
# Counts_84_DOX_24 <- readRDS("data/counts/Counts_84_DOX_24.RDS")
# Counts_84_DMSO_24 <- readRDS("data/counts/Counts_84_DMSO_24.RDS")
# Counts_84_DOX_24rec <- readRDS("data/counts/Counts_84_DOX_24rec.RDS")
# Counts_84_DMSO_24rec <- readRDS("data/counts/Counts_84_DMSO_24rec.RDS")
# Counts_84_DOX_144rec <- readRDS("data/counts/Counts_84_DOX_144rec.RDS")
# Counts_84_DMSO_144rec <- readRDS("data/counts/Counts_84_DMSO_144rec.RDS")
# 
# ####Individual 2 - 87-1####
# Counts_87_DOX_24 <- readRDS("data/counts/Counts_87_DOX_24.RDS")
# Counts_87_DMSO_24 <- readRDS("data/counts/Counts_87_DMSO_24.RDS")
# Counts_87_DOX_24rec <- readRDS("data/counts/Counts_87_DOX_24rec.RDS")
# Counts_87_DMSO_24rec <- readRDS("data/counts/Counts_87_DMSO_24rec.RDS")
# Counts_87_DOX_144rec <- readRDS("data/counts/Counts_87_DOX_144rec.RDS")
# Counts_87_DMSO_144rec <- readRDS("data/counts/Counts_87_DMSO_144rec.RDS")
# 
# ####Individual 3 - 78-1####
# Counts_78_DOX_24 <- readRDS("data/counts/Counts_78_DOX_24.RDS")
# Counts_78_DMSO_24 <- readRDS("data/counts/Counts_78_DMSO_24.RDS")
# Counts_78_DOX_24rec <- readRDS("data/counts/Counts_78_DOX_24rec.RDS")
# Counts_78_DMSO_24rec <- readRDS("data/counts/Counts_78_DMSO_24rec.RDS")
# Counts_78_DOX_144rec <- readRDS("data/counts/Counts_78_DOX_144rec.RDS")
# Counts_78_DMSO_144rec <- readRDS("data/counts/Counts_78_DMSO_144rec.RDS")
# 
# ####Individual 4 - 75-1####
# Counts_75_DOX_24 <- readRDS("data/counts/Counts_75_DOX_24.RDS")
# Counts_75_DMSO_24 <- readRDS("data/counts/Counts_75_DMSO_24.RDS")
# Counts_75_DOX_24rec <- readRDS("data/counts/Counts_75_DOX_24rec.RDS")
# Counts_75_DMSO_24rec <- readRDS("data/counts/Counts_75_DMSO_24rec.RDS")
# Counts_75_DOX_144rec <- readRDS("data/counts/Counts_75_DOX_144rec.RDS")
# Counts_75_DMSO_144rec <- readRDS("data/counts/Counts_75_DMSO_144rec.RDS")
# 
# ####Individual 5 - 17-3####
# Counts_17_DOX_24 <- readRDS("data/counts/Counts_17_DOX_24.RDS")
# Counts_17_DMSO_24 <- readRDS("data/counts/Counts_17_DMSO_24.RDS")
# Counts_17_DOX_24rec <- readRDS("data/counts/Counts_17_DOX_24rec.RDS")
# Counts_17_DMSO_24rec <- readRDS("data/counts/Counts_17_DMSO_24rec.RDS")
# Counts_17_DOX_144rec <- readRDS("data/counts/Counts_17_DOX_144rec.RDS")
# Counts_17_DMSO_144rec <- readRDS("data/counts/Counts_17_DMSO_144rec.RDS")
# 
# ####Individual 6 - 90-1####
# Counts_90_DOX_24 <- readRDS("data/counts/Counts_90_DOX_24.RDS")
# Counts_90_DMSO_24 <- readRDS("data/counts/Counts_90_DMSO_24.RDS")
# Counts_90_DOX_24rec <- readRDS("data/counts/Counts_90_DOX_24rec.RDS")
# Counts_90_DMSO_24rec <- readRDS("data/counts/Counts_90_DMSO_24rec.RDS")
# Counts_90_DOX_144rec <- readRDS("data/counts/Counts_90_DOX_144rec.RDS")
# Counts_90_DMSO_144rec <- readRDS("data/counts/Counts_90_DMSO_144rec.RDS")
# 
# ####Individual 7 - 90-1REP####
# Counts_90REP_DOX_24 <- readRDS("data/counts/Counts_90REP_DOX_24.RDS")
# Counts_90REP_DMSO_24 <- readRDS("data/counts/Counts_90REP_DMSO_24.RDS")
# Counts_90REP_DOX_24rec <- readRDS("data/counts/Counts_90REP_DOX_24rec.RDS")
# Counts_90REP_DMSO_24rec <- readRDS("data/counts/Counts_90REP_DMSO_24rec.RDS")
# Counts_90REP_DOX_144rec <- readRDS("data/counts/Counts_90REP_DOX_144rec.RDS")
# Counts_90REP_DMSO_144rec <- readRDS("data/counts/Counts_90REP_DMSO_144rec.RDS")

##Create my Dataframe from Counts Files

# counts_raw_df <-
#    data.frame(
#      Counts_84_DOX_24,
#      Counts_84_DMSO_24$MCW_EMP_JT_R29_R1.bam,
#      Counts_84_DOX_24rec$MCW_EMP_JT_R30_R1.bam,
#      Counts_84_DMSO_24rec$MCW_EMP_JT_R32_R1.bam,
#      Counts_84_DOX_144rec$MCW_EMP_JT_R33_R1.bam,
#      Counts_84_DMSO_144rec$MCW_EMP_JT_R35_R1.bam,
#      Counts_87_DOX_24$MCW_EMP_JT_R36_R1.bam,
#      Counts_87_DMSO_24$MCW_EMP_JT_R38_R1.bam,
#      Counts_87_DOX_24rec$MCW_EMP_JT_R39_R1.bam,
#      Counts_87_DMSO_24rec$MCW_EMP_JT_R41_R1.bam,
#      Counts_87_DOX_144rec$MCW_EMP_JT_R42_R1.bam,
#      Counts_87_DMSO_144rec$MCW_EMP_JT_R44_R1.bam,
#      Counts_78_DOX_24$MCW_EMP_JT_R45_R1.bam,
#      Counts_78_DMSO_24$MCW_EMP_JT_R47_R1.bam,
#      Counts_78_DOX_24rec$MCW_EMP_JT_R48_R1.bam,
#      Counts_78_DMSO_24rec$MCW_EMP_JT_R50_R1.bam,
#      Counts_78_DOX_144rec$MCW_EMP_JT_R51_R1.bam,
#      Counts_78_DMSO_144rec$MCW_EMP_JT_R53_R1.bam,
#      Counts_75_DOX_24$MCW_EMP_JT_R54_R1.bam,
#      Counts_75_DMSO_24$MCW_EMP_JT_R56_R1.bam,
#      Counts_75_DOX_24rec$MCW_EMP_JT_R57_R1.bam,
#      Counts_75_DMSO_24rec$MCW_EMP_JT_R59_R1.bam,
#      Counts_75_DOX_144rec$MCW_EMP_JT_R60_R1.bam,
#      Counts_75_DMSO_144rec$MCW_EMP_JT_R62_R1.bam,
#      Counts_17_DOX_24$MCW_EMP_JT_R63_R1.bam,
#      Counts_17_DMSO_24$MCW_EMP_JT_R65_R1.bam,
#      Counts_17_DOX_24rec$MCW_EMP_JT_R66_R1.bam,
#      Counts_17_DMSO_24rec$MCW_EMP_JT_R68_R1.bam,
#      Counts_17_DOX_144rec$MCW_EMP_JT_R69_R1.bam,
#      Counts_17_DMSO_144rec$MCW_EMP_JT_R71_R1.bam,
#      Counts_90_DOX_24$MCW_EMP_JT_R72_R1.bam,
#      Counts_90_DMSO_24$MCW_EMP_JT_R74_R1.bam,
#      Counts_90_DOX_24rec$MCW_EMP_JT_R75_R1.bam,
#      Counts_90_DMSO_24rec$MCW_EMP_JT_R77_R1.bam,
#      Counts_90_DOX_144rec$MCW_EMP_JT_R78_R1.bam,
#      Counts_90_DMSO_144rec$MCW_EMP_JT_R80_R1.bam,
#      Counts_90REP_DOX_24$MCW_EMP_JT_R81_R1.bam,
#      Counts_90REP_DMSO_24$MCW_EMP_JT_R83_R1.bam,
#      Counts_90REP_DOX_24rec$MCW_EMP_JT_R84_R1.bam,
#      Counts_90REP_DMSO_24rec$MCW_EMP_JT_R86_R1.bam,
#      Counts_90REP_DOX_144rec$MCW_EMP_JT_R87_R1.bam,
#      Counts_90REP_DMSO_144rec$MCW_EMP_JT_R89_R1.bam
#    )

#now save this as a matrix
#counts_raw_matrix <- counts_raw_df %>% column_to_rownames(var = "X") %>% as.matrix()

counts_raw_matrix <- readRDS("data/new/counts_raw_matrix.RDS")

dim(counts_raw_matrix)

[1] 28395    42

#28395 is my initial amount of genes prior to filtering

#write this to a csv so I can save it for later
#write.csv(counts_raw_matrix, "C:/Users/emmap/RDirectory/Recovery_RNAseq/Recovery_5FU/data/new/counts_raw_matrix_EMP_250514.csv")

#I also want to save this as an R object so I don't have to run the counts every time
#saveRDS(counts_raw_matrix, "data/new/counts_raw_matrix.RDS")

###Include colors and factors for analysis

#I want to include the color schemes I have for my treatment, individuals, and timepoints
####Colors####
tx_col <- c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")
col_tx_large <- rep(c("#499FBD" , "#BBBBBC"), 21)
col_tx_large_2 <- c(rep("#499FBD" , 3), rep("#BBBBBC", 3), 21)

ind_col <- c("#003F5C", "#45AE91",  "#58209D", "#8B3E9B", "#FF6361", "#BC4169", "#FF2362")

ind_col_norep <- c("#003F5C", "#45AE91",  "#58209D", "#8B3E9B", "#FF6361", "#BC4169")

time_col <- c("#238B45", "#74C476", "#C7E9C0")

cond_col <- c("#003F5C", "#45AE91",  "#58209D", "#8B3E9B", "#FF6361", "#BC4169")

#QC Mapping Plots

#this dataframe contains my alignment percentages from featureCounts
##already filtered to only include DOX + DMSO samples
fC_DOXCounts <- readRDS("data/fC_DOXCounts.RDS")

#Now I want to plot these values out

####Reads by Sample####
reads_by_sample <- c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")
fC_DOXCounts %>% 
  ggplot(., aes (x = Conditions, y = Total_Align, fill = Treatment, group_by = Line))+
  geom_col()+
 geom_hline(aes(yintercept=20000000))+
 scale_fill_manual(values=reads_by_sample)+
  ggtitle(expression("Total number of reads by sample"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 90, hjust = 1, vjust = 0.2),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Read Counts by Treatment####
fC_DOXCounts %>% 
  ggplot(., aes (x =Treatment, y= Total_Align, fill = Treatment))+
  geom_boxplot()+
 scale_fill_manual(values=reads_by_sample)+
  ggtitle(expression("Total number of reads by treatment"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+
  
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 90, hjust = 1, vjust = 0.2),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Total Reads Per Individual####
fC_DOXCounts %>% 
  ggplot(., aes (x =as.factor(Line), y=Total_Align))+
  geom_boxplot(aes(fill=as.factor(Line)))+
 scale_fill_brewer(palette = "Dark2", name = "Individual")+
  ggtitle(expression("Total number of reads by individual"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+

  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 0, hjust = 1),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-3.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Total Mapped Reads Per Drug####

reads_by_sample <- c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")
fC_DOXCounts %>% 
  ggplot(., aes (x = Conditions, y = Assigned_Align, fill = Treatment, group_by = Line))+
  geom_col()+
 geom_hline(aes(yintercept=20000000))+
 scale_fill_manual(values=reads_by_sample)+
  ggtitle(expression("Total number of mapped reads by sample"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 90, hjust = 1, vjust = 0.2),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-4.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Read Counts by Treatment####
fC_DOXCounts %>% 
  ggplot(., aes (x =Treatment, y= Assigned_Align, fill = Treatment))+
  geom_boxplot()+
 scale_fill_manual(values=reads_by_sample)+
  ggtitle(expression("Total number of mapped reads by treatment"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+
  
  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 90, hjust = 1, vjust = 0.2),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-5.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Total Reads Per Individual####
fC_DOXCounts %>% 
  ggplot(., aes (x =as.factor(Line), y=Assigned_Align))+
  geom_boxplot(aes(fill=as.factor(Line)))+
 scale_fill_brewer(palette = "Dark2", name = "Individual")+
  ggtitle(expression("Total number of mapped reads by individual"))+
  xlab("")+
  ylab(expression("RNA-sequencing reads"))+
  theme_bw()+

  theme(plot.title = element_text(size = rel(2), hjust = 0.5),
        axis.title = element_text(size = 15, color = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.text.y = element_text(size =10, color = "black", angle = 0, hjust = 0.8, vjust = 0.5),
        axis.text.x = element_text(size =10, color = "black", angle = 0, hjust = 1),
        #strip.text.x = element_text(size = 15, color = "black", face = "bold"),
        strip.text.y = element_text(color = "white"))

Past versions of "QC Mapping Plots-6.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Now, I want to filter my dataframe Before I can filter by rowMeans, I must convert to log2cpm #Filter my Dataframe and Convert to log2cpm

#transform counts to cpm as a first step
counts_cpm_unfilt <- cpm(counts_raw_matrix, log = TRUE)
dim(counts_cpm_unfilt)

[1] 28395    42

#I should have 28395 genes here since this is unfiltered

hist(counts_cpm_unfilt,  
     main = "Histogram of Unfiltered Counts", 
     xlab = expression("Log"[2]*" counts-per-million"), 
     col = 4)

Past versions of "Dataframe Filtering-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

###filter my data by rowMeans > 0 to exclude lowly expressed genes

filcpm_matrix <- subset(counts_cpm_unfilt, (rowMeans(counts_cpm_unfilt) > 0))
dim(filcpm_matrix)

[1] 14319    42

#I should have 14319 genes here

#now let's make a histogram of this to check the difference
hist(filcpm_matrix,  
     main = "Histogram of Filtered Counts by rowMeans > 0", 
     xlab = expression("Log"[2]*" counts-per-million"), 
     col = 2)

Past versions of "Dataframe Filtering-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#change the column names to match my samples - make sure that they are in the right order
#Individual 1 = 84-1 (M)
#Individual 2 = 87-1 (F)
#Individual 3 = 78-1 (F)
#Individual 4 = 75-1 (F)
#Individual 5 = 17-3 (M)
#Individual 6 = 90-1 (M)
#Individual 6REP = 90-1REP (M)

#Treatment/time should follow this order:
#DOX24tx
#DMSO24tx
#DOX24rec
#DMSO24rec
#DOX144rec
#DMSO144rec

colnames(filcpm_matrix) <- c("DOX_24T_Ind1",
                                "DMSO_24T_Ind1",
                                "DOX_24R_Ind1",
                                "DMSO_24R_Ind1",
                                "DOX_144R_Ind1",
                                "DMSO_144R_Ind1",
                                "DOX_24T_Ind2",
                                "DMSO_24T_Ind2",
                                "DOX_24R_Ind2",
                                "DMSO_24R_Ind2",
                                "DOX_144R_Ind2",
                                "DMSO_144R_Ind2",
                                "DOX_24T_Ind3",
                                "DMSO_24T_Ind3",
                                "DOX_24R_Ind3",
                                "DMSO_24R_Ind3",
                                "DOX_144R_Ind3",
                                "DMSO_144R_Ind3",
                                "DOX_24T_Ind4",
                                "DMSO_24T_Ind4",
                                "DOX_24R_Ind4",
                                "DMSO_24R_Ind4",
                                "DOX_144R_Ind4",
                                "DMSO_144R_Ind4",
                                "DOX_24T_Ind5",
                                "DMSO_24T_Ind5",
                                "DOX_24R_Ind5",
                                "DMSO_24R_Ind5",
                                "DOX_144R_Ind5",
                                "DMSO_144R_Ind5",
                                "DOX_24T_Ind6",
                                "DMSO_24T_Ind6",
                                "DOX_24R_Ind6",
                                "DMSO_24R_Ind6",
                                "DOX_144R_Ind6",
                                "DMSO_144R_Ind6",
                                "DOX_24T_Ind6REP",
                                "DMSO_24T_Ind6REP",
                                "DOX_24R_Ind6REP",
                                "DMSO_24R_Ind6REP",
                                "DOX_144R_Ind6REP",
                                "DMSO_144R_Ind6REP")

#export this as a csv
#write.csv(filcpm_matrix, "data/new/filcpm_final_matrix.csv")

##QC Boxplots of Filtered vs Unfiltered Data

#make boxplots of all counts vs log2cpm filtered counts

#set the margins so the x axis isn't cut off
##I don't mind if this one is partially cut off since all you need is the library number and not the whole name
par(mar = c(8,4,2,2))
#boxplot of unfiltered cpm matrix
boxplot(counts_cpm_unfilt, 
        main = "Boxplots of Unfiltered log2cpm", 
        names = colnames(counts_cpm_unfilt), 
        adj=1, las = 2, cex.axis = 0.7)

Past versions of "QC Filtering Boxplots-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#set the margins so the x axis isn't cut off
par(mar = c(8,4,2,2))
#boxplot of filtered cpm matrix
boxplot(filcpm_matrix, 
        main = "Boxplots of Filtered log2cpm (rowMeans > 0)", 
        names = colnames(filcpm_matrix), 
        adj=1, las = 2, cex.axis = 0.7)

Past versions of "QC Filtering Boxplots-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

After making my final matrix, I pulled the gene symbols from the entrez IDs I had as my rownames I ran this initially and then moved the column into my final matrix My final matrix is called filcpm_final_matrix.csv saved under data #Put together my Data for Filtered Gene List

##I did this earlier so don't run again, I put the list into the filcpm_final_matrix.csv
# # ----------------- Load Required Libraries -----------------
# library(dplyr)
# library(readr)
# library(org.Hs.eg.db)
# library(AnnotationDbi)
# # ----------------- Load Data -----------------
# sample_data <- read_csv("data/filcpm_final_matrix.csv", show_col_types = FALSE)
# # ----------------- Ensure Entrez_ID is Present and in Character Format -----------------
# # Check column names
# print(colnames(sample_data))
# # Rename if needed (adjust if the column name is not exactly 'Entrez_ID')
# # sample_data <- sample_data %>% rename(Entrez_ID = `actual_column_name`)
# # Convert Entrez_ID to character
# sample_data <- sample_data %>%
#   mutate(Entrez_ID = as.character(Entrez_ID))
# # ----------------- Map Entrez_ID to Gene Symbol -----------------
# gene_symbols <- AnnotationDbi::select(
#   org.Hs.eg.db,
#   keys = sample_data$Entrez_ID,
#   columns = c("SYMBOL"),
#   keytype = "ENTREZID"
# )
# # ----------------- Join Back to Main Data -----------------
# sample_annotated <- left_join(sample_data, gene_symbols, by = c("Entrez_ID" = "ENTREZID"))
# # ----------------- Save Annotated Output -----------------
# #write_csv(sample_annotated, "data/Sample_annotated.csv")

#Since I ran this before, Sample_annotated.csv columns of EntrezID and Symbol have been copied into my final matrix - so disregard this file except for record-keeping

Now that I have my final matrix, I would like to check some key genes I want to make sure that these genes are responding as we expect We have triple checked this dataset to ensure that columns are in order #Check my Response Genes in log2cpm format

#Load in my count matrix
boxplot1 <- read.csv("data/new/filcpm_final_matrix.csv") %>% 
  as.data.frame()

#save boxplot1 as an object filcpm_matrix_genes
#saveRDS(boxplot1, "data/new/filcpm_matrix_genes.RDS")

#Define gene list(s)
initial_test_genes <- c("CDKN1A", "MDM2", "BAX", "RARG", "TP53", "TOP2B", "TOP2A")  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_data <- function(gene) {
  gene_data <- boxplot1 %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#this function is saved under process_gene_data so I will save as an R object

#saveRDS(process_gene_data, "data/new/process_gene_data_funct.RDS")

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes) {
  gene_data <- process_gene_data(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression of", gene)) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "Check Response Genes log2cpm-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Past versions of "Check Response Genes log2cpm-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Past versions of "Check Response Genes log2cpm-3.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Past versions of "Check Response Genes log2cpm-4.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Past versions of "Check Response Genes log2cpm-5.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

Past versions of "Check Response Genes log2cpm-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Check Response Genes log2cpm-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Now I’ve confirmed with some boxplots that my genes are present and (mostly) behaving as they should - Sayan’s CDKN1A and MDM2 are initially high at 24hr in DOX 0.5 - My CDKN1A and MDM2 are similar to DMSO at 24hr DOX 0.5 - These genes increase at DOX24R - These genes are also high at DOX144R but not as high as 24R However, TP53 and BAX are acting similarly across our data #PCA Analysis

#Now I want to check if my data is as expected on a PCA plot
#perform PCA calculations
prcomp_res_unfilt <- prcomp(t(counts_cpm_unfilt %>% as.matrix()), center =  TRUE)

prcomp_res_filt <- prcomp(t(filcpm_matrix %>% as.matrix()), center =  TRUE)

#read in my metadata annotations
Metadata <- read.csv("data/new/Metadata.csv")

#add in labels for individual numbers
ind_num <- c("1", "1", "1", "1", "1", "1", 
             "2", "2", "2", "2", "2", "2", 
             "3", "3", "3", "3", "3", "3", 
             "4", "4", "4", "4", "4", "4", 
             "5", "5", "5", "5", "5", "5", 
             "6", "6", "6", "6", "6", "6", 
             "6R", "6R", "6R", "6R", "6R", "6R")

# saveRDS(ind_num, "data/new/ind_num.RDS")

#now plot my PCA for unfiltered log2cpm
####PC1/PC2####
ggplot2::autoplot(prcomp_res_unfilt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=1, y=2) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Unfiltered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-1.png"

Version	Author	Date
14cdab3	emmapfort	2025-07-02
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

####PC2/PC3####
ggplot2::autoplot(prcomp_res_unfilt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=2, y=3) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Unfiltered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

####PC3/PC4####
ggplot2::autoplot(prcomp_res_unfilt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=3, y=4) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Unfiltered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

#Now plot my PCA for filtered log2cpm
####PC1/PC2####
ggplot2::autoplot(prcomp_res_filt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=1, y=2) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

ggplot2::autoplot(prcomp_res_filt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=1, y=2) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

####PC2/PC3####
ggplot2::autoplot(prcomp_res_filt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=2, y=3) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08
1b8f045	emmapfort	2025-07-03
0b1ffad	emmapfort	2025-07-02
29a5c35	emmapfort	2025-05-16

####PC3/PC4####
ggplot2::autoplot(prcomp_res_filt, data = Metadata, colour = "Condition", shape = "Time", size =4, x=3, y=4) +
  ggrepel::geom_text_repel(label=ind_num, vjust = -.5, max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered log"[2]*"cpm")) +
  theme_bw()

Past versions of "PCA Analysis-7.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08
1b8f045	emmapfort	2025-07-03
0b1ffad	emmapfort	2025-07-02

#Correlation Heatmaps

#check to make sure that the column names are correct
lcpm_2 <- filcpm_matrix
colnames(lcpm_2) <- Metadata$Final_sample_name

#compute the correlation matrices, one pearson and one spearman
cor_matrix_pearson <- cor(lcpm_2, 
                          y = NULL, 
                          use = "everything",  
                          method = "pearson")
cor_matrix_spearman <- cor(lcpm_2,
                           y = NULL,
                           use = "everything",
                           method = "spearman")

# Extract metadata columns
Individual <- as.character(Metadata$Ind)
Time <- as.character(Metadata$Time)
Treatment <- as.character(Metadata$Drug)

# Define color palettes for annotations
annot_col_cor = list(drugs = c("DOX" = "#499FBD", 
                               "DMSO" = "#BBBBBC"),
                     individuals = c("1" = "#003F5C", 
                                     "2" = "#45AE91", 
                                     "3" = "#58209D", 
                                     "4" = "#8B3E9B", 
                                     "5" = "#FF6361", 
                                     "6" = "#BC4169", 
                                     "6R" = "#FF2362"),
                     timepoints = c("24T" = "#238B45",
                                    "24R" = "#74C476", 
                                    "144R" = "#C7E9C0"))

drug_colors <- c("DOX" = "#499FBD", 
                 "DMSO" = "#BBBBBC")
ind_colors <- c("1" = "red",
                "2" = "orange",
                "3" = "yellow",
                "4" = "green",
                "5" = "blue",
                "6" = "violet",
                "6R" = "purple")
time_colors <- c("24T" = "#238B45",
                 "24R" = "#74C476",
                 "144R" = "#C7E9C0")

# Create annotations
top_annotation <- HeatmapAnnotation(
  Individual = Individual, 
  Time = Time,
  Treatment = Treatment,
  col = list(
    Individual = ind_colors, 
    Time = time_colors,
    Treatment = drug_colors
  )
)

####ANNOTATED HEATMAPS####
# pheatmap(cor_matrix_pearson, border_color = "black", legend = TRUE, angle_col = 90, display_numbers = FALSE, number_color = "black", fontsize = 10, fontsize_number = 5, annotation_col = top_annotation, annotation_colors = annot_col)

####Pearson Heatmap####
heatmap_pearson <- Heatmap(cor_matrix_pearson,
                           name = "Pearson",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE)

# Draw the heatmap
draw(heatmap_pearson)

Past versions of "Correlation Heatmaps-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

####Spearman Heatmap####
heatmap_spearman <- Heatmap(cor_matrix_spearman,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE)

# Draw the heatmap
draw(heatmap_spearman)

Past versions of "Correlation Heatmaps-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#Make my Filtered Gene List

#Now I want to make a filtered gene list (my rownames)
##I will use this to filter my counts for limma + Cormotif

filt_gene_list <- rownames(filcpm_matrix)
#save this filtered gene list as I'll use it to filter my counts
#saveRDS(filt_gene_list, "data/new/filt_gene_list.RDS")

##Filter my Counts For DE Analysis

counts_raw_matrix <- readRDS("data/new/counts_raw_matrix.RDS")
#change column names to match samples for my raw counts matrix
colnames(counts_raw_matrix) <- c("DOX_24T_Ind1",
                                "DMSO_24T_Ind1",
                                "DOX_24R_Ind1",
                                "DMSO_24R_Ind1",
                                "DOX_144R_Ind1",
                                "DMSO_144R_Ind1",
                                "DOX_24T_Ind2",
                                "DMSO_24T_Ind2",
                                "DOX_24R_Ind2",
                                "DMSO_24R_Ind2",
                                "DOX_144R_Ind2",
                                "DMSO_144R_Ind2",
                                "DOX_24T_Ind3",
                                "DMSO_24T_Ind3",
                                "DOX_24R_Ind3",
                                "DMSO_24R_Ind3",
                                "DOX_144R_Ind3",
                                "DMSO_144R_Ind3",
                                "DOX_24T_Ind4",
                                "DMSO_24T_Ind4",
                                "DOX_24R_Ind4",
                                "DMSO_24R_Ind4",
                                "DOX_144R_Ind4",
                                "DMSO_144R_Ind4",
                                "DOX_24T_Ind5",
                                "DMSO_24T_Ind5",
                                "DOX_24R_Ind5",
                                "DMSO_24R_Ind5",
                                "DOX_144R_Ind5",
                                "DMSO_144R_Ind5",
                                "DOX_24T_Ind6",
                                "DMSO_24T_Ind6",
                                "DOX_24R_Ind6",
                                "DMSO_24R_Ind6",
                                "DOX_144R_Ind6",
                                "DMSO_144R_Ind6",
                                "DOX_24T_Ind6REP",
                                "DMSO_24T_Ind6REP",
                                "DOX_24R_Ind6REP",
                                "DMSO_24R_Ind6REP",
                                "DOX_144R_Ind6REP",
                                "DMSO_144R_Ind6REP")


#subset my count matrix based on filtered CPM matrix
x <- counts_raw_matrix[row.names(filcpm_matrix),]
dim(x)

[1] 14319    42

#14319 genes as expected!
#this is still in counts form

#remove my replicate individual at this time
x_norep <- x[,1:36]

#modify my metadata to match
Metadata_2 <- Metadata[1:36,]
rownames(Metadata_2) <- Metadata_2$Sample_bam
colnames(x_norep) <- Metadata_2$Sample_ID
rownames(Metadata_2) <- Metadata_2$Sample_ID

Metadata_2$Condition <- make.names(Metadata_2$Condition)
Metadata_2$Ind <- as.character(Metadata_2$Ind)

#saveRDS(Metadata_2, "data/new/Metadata_2_norep.RDS")

#Perform Differential Expression Analysis

#create DGEList object
dge <- DGEList(counts = x_norep)
dge$samples$group <- factor(Metadata_2$Condition)
dge <- calcNormFactors(dge, method = "TMM")

#saveRDS(dge, "data/new/dge_matrix.RDS")

#check normalization factors from TMM normalization of LIBRARIES
dge$samples

                     group lib.size norm.factors
84-1_DOX_24        DOX_24T 23393931    0.9745263
84-1_DMSO_24      DMSO_24T 22853195    0.9565797
84-1_DOX_24+24     DOX_24R 23846995    1.1659432
84-1_DMSO_24+24   DMSO_24R 21299355    0.9649641
84-1_DOX_24+144   DOX_144R 18222568    0.9913625
84-1_DMSO_24+144 DMSO_144R 28115884    0.9653464
87-1_DOX_24        DOX_24T 19935097    1.0526605
87-1_DMSO_24      DMSO_24T 21302879    0.9773889
87-1_DOX_24+24     DOX_24R 25636959    1.0751043
87-1_DMSO_24+24   DMSO_24R 26319662    0.9940323
87-1_DOX_24+144   DOX_144R 23463426    0.9003102
87-1_DMSO_24+144 DMSO_144R 25840938    0.9888449
78-1_DOX_24        DOX_24T 23085807    0.7676077
78-1_DMSO_24      DMSO_24T 25610495    1.0077383
78-1_DOX_24+24     DOX_24R 18083930    1.1682704
78-1_DMSO_24+24   DMSO_24R 24331177    0.9906872
78-1_DOX_24+144   DOX_144R 19754391    0.9941834
78-1_DMSO_24+144 DMSO_144R 22641509    1.0010734
75-1_DOX_24        DOX_24T 20583626    1.0676786
75-1_DMSO_24      DMSO_24T 28166198    1.0031906
75-1_DOX_24+24     DOX_24R 25831427    1.1530208
75-1_DMSO_24+24   DMSO_24R 26081158    1.0058953
75-1_DOX_24+144   DOX_144R 24659898    0.9261599
75-1_DMSO_24+144 DMSO_144R 25412931    0.9703454
17-3_DOX_24        DOX_24T 22518848    0.9766893
17-3_DMSO_24      DMSO_24T 24589534    0.9612345
17-3_DOX_24+24     DOX_24R 24797547    1.1703079
17-3_DMSO_24+24   DMSO_24R 25977536    0.9509690
17-3_DOX_24+144   DOX_144R 27447106    0.9422729
17-3_DMSO_24+144 DMSO_144R 24893583    0.9356377
90-1_DOX_24        DOX_24T 25187428    1.0311957
90-1_DMSO_24      DMSO_24T 25630519    1.0283437
90-1_DOX_24+24     DOX_24R 26138399    1.1183471
90-1_DMSO_24+24   DMSO_24R 24430396    0.9988688
90-1_DOX_24+144   DOX_144R 23323463    0.9496884
90-1_DMSO_24+144 DMSO_144R 25424152    0.9872926

#create my design matrix for DE
design <- model.matrix(~ 0 + Metadata_2$Condition)
colnames(design) <- gsub("Metadata_2\\$Condition", "", colnames(design))

#take care that the matrix automatically sorts cols alphabetically
##currently DMSO144R, DMSO24R, DMSO24T, DOX144R, DOX24R, DOX24T

#run duplicate correlation for individual effect
corfit <- duplicateCorrelation(object = dge$counts, design = design, block = Metadata_2$Ind)

#voom transformation and plot
v <- voom(dge, design, block = Metadata_2$Ind, correlation = corfit$consensus.correlation, plot = TRUE)

Past versions of "Differential Expression Analysis-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#fit my linear model
fit <- lmFit(v, design, block = Metadata_2$Ind, correlation = corfit$consensus.correlation)

#make my contrast matrix to compare across tx and veh
contrast_matrix <- makeContrasts(
  V.D24T = DOX_24T - DMSO_24T,
  V.D24R = DOX_24R - DMSO_24R, 
  V.D144R = DOX_144R - DMSO_144R,
  levels = design
)

#apply these contrasts to compare DOX to DMSO VEH
fit2 <- contrasts.fit(fit, contrast_matrix)
fit2 <- eBayes(fit2)

#plot the mean-variance trend
plotSA(fit2, main = "Final model: Mean-Variance trend")

Past versions of "Differential Expression Analysis-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#look at the summary of your results
##this tells you the number of DEGs in each condition
results_summary <- decideTests(fit2, adjust.method = "BH", p.value = 0.05)
summary(results_summary)

       V.D24T V.D24R V.D144R
Down     4723   3593     359
NotSig   5076   7151   13810
Up       4520   3575     150

#        V.D24 V.D24r V.D144r
# Down    4723   3593     359
# NotSig  5076   7151   13810
# Up      4520   3575     150

vennDiagram(object = results_summary, include = c("up", "down"))

Past versions of "Differential Expression Analysis-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Create Toptables of my DEGs

# Generate Top Table for Specific Comparisons

Toptable_V.D24T <- topTable(fit = fit2, coef = "V.D24T", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D24T, "data/new/DEGs/Toptable_V.D24T.csv")

Toptable_V.D24R <- topTable(fit = fit2, coef = "V.D24R", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D24R, "data/new/DEGs/Toptable_V.D24R.csv")

Toptable_V.D144R <- topTable(fit = fit2, coef = "V.D144R", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D144R, "data/new/DEGs/Toptable_V.D144R.csv")

#save all of these toptables as R objects
# saveRDS(list(
#   V.D24T = Toptable_V.D24T,
#   V.D24R = Toptable_V.D24R,
#   V.D144R = Toptable_V.D144R
# ), file = "data/new/Toptable_list.RDS")

Toptable_list <- readRDS("data/new/Toptable_list.RDS")

##Top 5 DEGs after DE Analysis per Condition

#use your three toptables so I can pull out top 5 genes from each based on adj. p val

top5_D24T <- Toptable_V.D24T[order(Toptable_V.D24T$adj.P.Val), ][1:5,] %>% 
  rownames_to_column(., var = "Entrez_ID")
top5_D24R <- Toptable_V.D24R[order(Toptable_V.D24R$adj.P.Val), ][1:5,] %>% 
  rownames_to_column(., var = "Entrez_ID")
top5_D144R <- Toptable_V.D144R[order(Toptable_V.D144R$adj.P.Val), ][1:5,] %>% 
  rownames_to_column(., var = "Entrez_ID")

#now that I've pulled the top 5 DEGs from each, make a list to pull them from my log2cpm data

boxplot1 <- read.csv("data/new/filcpm_final_matrix.csv") %>% 
  as.data.frame()

#Define gene list
#these are the top 5 genes pulled from my toptables
top5_D24T_geneslist <- c(top5_D24T$Entrez_ID)
top5_D24R_geneslist <- c(top5_D24R$Entrez_ID)
top5_D144R_geneslist <- c(top5_D144R$Entrez_ID)
#Add more gene symbols as needed or add more categories

#now pull these from my log2cpm matrix
top5_D24T_genes <- boxplot1[boxplot1$Entrez_ID %in% top5_D24T_geneslist,]
dim(top5_D24T_genes)

[1]  5 44

#5 genes in 44 cols
top5_D24R_genes <- boxplot1[boxplot1$Entrez_ID %in% top5_D24R_geneslist,]
dim(top5_D24R_genes)

[1]  5 44

#5 genes in 44 cols
top5_D144R_genes <- boxplot1[boxplot1$Entrez_ID %in% top5_D144R_geneslist,]
dim(top5_D144R_genes)

[1]  5 44

#5 genes in 44 cols

#Now put in the function I want to use to generate boxplots of genes
#####D24T#####
process_top5_D24T <- function(gene) {
  gene_data <- top5_D24T_genes %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D24T_geneslist) {
  gene_data <- process_top5_D24T(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm Expression of", gene, "top 5 DEGs D24T")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "Top 5 DEGs Limma-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####D24R#####
process_top5_D24R <- function(gene) {
  gene_data <- top5_D24R_genes %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D24R_geneslist) {
  gene_data <- process_top5_D24R(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm Expression of", gene, "top 5 DEGs D24R")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "Top 5 DEGs Limma-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-10.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####D144R#####
process_top5_D144R <- function(gene) {
  gene_data <- top5_D144R_genes %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D144R_geneslist) {
  gene_data <- process_top5_D144R(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm Expression of", gene, "top 5 DEGs D144R")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "Top 5 DEGs Limma-11.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-12.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-13.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-14.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Top 5 DEGs Limma-15.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##LogFC Boxplots for All Conditions

# Toptable_V.D24T

# Load DEGs Data
DOX_24T <- read.csv("data/new/DEGs/Toptable_V.D24T.csv")
DOX_24R <- read.csv("data/new/DEGs/Toptable_V.D24R.csv")
DOX_144R <- read.csv("data/new/DEGs/Toptable_V.D144R.csv")

#make a list of all of the genes in this set so I can plot the logFC in other sets
D24T_DEGs <- DOX_24T$Entrez_ID[DOX_24T$adj.P.Val < 0.05]
length(D24T_DEGs)

[1] 9243

#9243 genes in length after adj. p value cutoff
#if I did p value only - 9658 genes

#now that I have a list of my DEGs from D24T - pull these genes out from the other DEG lists
# D24R_DEGs <- Toptable_V.D24R[Toptable_V.D24R$adj.P.Val < 0.05,]

# D24R_DEGs_D24T <- D24R_DEGs %>%  
#   rownames_to_column(., var = "Entrez_ID")

# D24R_DEGs_D24T <- D24R_DEGs_D24T[D24R_DEGs_D24T$Entrez_ID %in% D24T_DEGs,]
# dim(D24R_DEGs_D24T)
#4831 genes in common here after adj p value cutoff

# D144R_DEGs <- Toptable_V.D144R[Toptable_V.D144R$adj.P.Val < 0.05,]
# 
# D144R_DEGs_D24T <- D144R_DEGs %>%  
#   rownames_to_column(., var = "Entrez_ID")
# 
# D144R_DEGs_D24T <- D144R_DEGs_D24T[D144R_DEGs_D24T$Entrez_ID %in% D24T_DEGs,]
# dim(D144R_DEGs_D24T)
#322 genes in common after adj p value cutoff

#now I want to plot the logFC of these

#ignore the above for now, just plot those full gene sets in logFC
D24T_DEGs <- DOX_24T$Entrez_ID[DOX_24T$adj.P.Val < 0.05]
length(D24T_DEGs)

[1] 9243

D24R_DEGs <- DOX_24R$Entrez_ID[DOX_24R$adj.P.Val < 0.05]
length(D24R_DEGs)

[1] 7168

D144R_DEGs <- DOX_144R$Entrez_ID[DOX_144R$adj.P.Val < 0.05]
length(D144R_DEGs)

[1] 509

#now that I have the full list of genes, I want to plot the logFC across conditions
#to do this - make a combined toptable

# Toptable_list

#plot the set of genes across conditions
# 
# logFC_long_allsets <- imap_dfr(Toptable_list, function(tbl, condition) {
#   tbl %>% 
#     rownames_to_column(var = "Entrez_ID") %>% 
#     dplyr::select(Entrez_ID, logFC) %>% 
#     mutate(Condition = condition)
# })
# 
# 
# ggplot(logFC_long_allsets, aes(x = Condition, y = logFC, group = Entrez_ID, color = Entrez_ID)) +
#   geom_boxplot() +
#   geom_point(size = 2) +
#   labs(
#     title = "logFC of Genes Across Conditions",
#     x = "Condition",
#     y = "logFC"
#   ) +
#   theme_minimal()


####Try this####

#Combine the toptables I have from pairwise analysis into a single dataframe
d24_toptable_dxr <- Toptable_V.D24T %>% 
  rownames_to_column(var = "Entrez_ID") %>% 
  mutate(Time = "24")

d24r_toptable_dxr <- Toptable_V.D24R %>% 
  rownames_to_column(var = "Entrez_ID") %>% 
  mutate(Time = "24R")

d144r_toptable_dxr <- Toptable_V.D144R %>% 
  rownames_to_column(var = "Entrez_ID") %>% 
  mutate(Time = "144R")

combined_toptables_dxr <- bind_rows(
  d24_toptable_dxr,
  d24r_toptable_dxr,
  d144r_toptable_dxr)

#Filter the data based on each motif
filt_toptable_dxr <- combined_toptables_dxr %>% 
  dplyr::filter(Entrez_ID  %in% D24T_DEGs) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for D24T DEGs Across Conditions")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#now do the same with the other conditions

filt_toptable_dxr_24r <- combined_toptables_dxr %>% 
  dplyr::filter(Entrez_ID  %in% D24R_DEGs) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for D24R DEGs Across Conditions")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#D144R

filt_toptable_dxr_144r <- combined_toptables_dxr %>% 
  dplyr::filter(Entrez_ID  %in% D144R_DEGs) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for D144R DEGs Across Conditions")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#now put the names of these graphs to print them
filt_toptable_dxr

Past versions of "DOX24T DEGs logFC all Conditions-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_dxr_24r

Past versions of "DOX24T DEGs logFC all Conditions-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_dxr_144r

Past versions of "DOX24T DEGs logFC all Conditions-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#Perform RUVs Correction ##Set Up Data and Perform PCAs on Un-normalized Data

filt_gene_list <- rownames(filcpm_matrix)
#14319 genes as usual

#in order to make this match with annot later down the line, change the col names for counts_raw_matrix to match final_sample_names in annot

#i'll also want to make sure I keep the replicate for this set

colnames(counts_raw_matrix) <- Metadata$Final_sample_name

RUV_filt_counts <- counts_raw_matrix %>% 
  as.data.frame() %>% 
  dplyr::filter(., row.names(.)%in% filt_gene_list)

#add in the annotation files
ind_num <- readRDS("data/new/ind_num.RDS")
annot <- read.csv("data/new/Metadata.csv")

#  counts need to be integer values and in a numeric matrix
# note: the log transformation needs to be accounted for in the isLog argument in RUVs function.
counts <- as.matrix(RUV_filt_counts)
#saveRDS(counts, "data/new/RUV/filt_counts_matrix.RDS")

# Create a DataFrame for the phenoData
phenoData <- DataFrame(annot)

# Now create the RangedSummarizedExperiment necessary for RUVs input
# looks like it did need both the phenodata and the counts.
set <- SummarizedExperiment(assays =  counts, metadata = phenoData)

# Generate a background matrix
# The column "Cond" holds the comparisons that you actually want to make. DOX_24, DMSO_24,5FU_24, DOX_3,etc.
scIdx <-RUVSeq::makeGroups(phenoData$Condition)
scIdx

     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]    6   12   18   24   30   36   42
[2,]    4   10   16   22   28   34   40
[3,]    2    8   14   20   26   32   38
[4,]    5   11   17   23   29   35   41
[5,]    3    9   15   21   27   33   39
[6,]    1    7   13   19   25   31   37

#now I've made all of the data I need for this - they are located in each section for k values

#DO NOT USE THESE COUNTS FOR LINEAR MODELING

#colors for all of the plots
fill_col_ind <- c("#66C2A5", "#FC8D62", "#1F78B4", "#E78AC3", "#A6D854", "#FFD92A", "#8B3E9B")

fill_col_ind_dark <- c("#003F5C", "#45AE91",  "#58508D", "#BC4099", "#8B3E9B", "#FF6361", "#FF2362")

fill_col_tx <- c("#63666D", "#499FBD", "#DCACED")

fill_col_txtime <- c("#003F5C", "#45AE91",  "#58508D", "#BC4099", "#8B3E9B", "#FF6361", "#FF2362", "#A6D854", "#FC8D62")

# before ruv (counts PCA)
prcomp_res_counts <- prcomp(t(counts), scale. = FALSE, center = TRUE)
annot_prcomp_res <- prcomp_res_counts$x %>% cbind(., annot)

group_2 <- annot$Condition

#now plot my PCA for filtered counts
####PC1/PC2####
ggplot2::autoplot(prcomp_res_counts, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1, 
                  y=2) +
  ggrepel::geom_text_repel(label=ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered Counts")) +
  theme_bw()

Past versions of "RUVs Correction Data Setup - no RUV yet-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####PC2/PC3####
ggplot2::autoplot(prcomp_res_counts, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3) +
  ggrepel::geom_text_repel(label=ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of Filtered Counts")) +
  theme_bw()

Past versions of "RUVs Correction Data Setup - no RUV yet-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#go ahead and plot PCA of log2cpm to compare (somewhat) later since the norm counts output isn't possible with these data since they don't undergo correction

prcomp_res_cpm <- prcomp(t(filcpm_matrix %>% as.matrix()), center =  TRUE)

####PC1/PC2####
ggplot2::autoplot(prcomp_res_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1, 
                  y=2) +
  ggrepel::geom_text_repel(label=ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of log2cpm no RUVs")) +
  theme_bw()

Past versions of "RUVs Correction Data Setup - no RUV yet-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####PC2/PC3####
ggplot2::autoplot(prcomp_res_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3) +
  ggrepel::geom_text_repel(label=ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30) +
  scale_color_manual(values=cond_col) +
  ggtitle(expression("PCA of log2cpm no RUVs")) +
  theme_bw()

Past versions of "RUVs Correction Data Setup - no RUV yet-4.png"

Version	Author	Date
14cdab3	emmapfort	2025-07-02
0b1ffad	emmapfort	2025-07-02

####new PCA plots no correction####
#PCA plots for each value of k attached in each section

#####Now start performing RUV 1-3###

##RUVs with k = 1

#Apply RUVs function from RUVSeq
#"k" will be iteratively adjusted over time depending on your PCA.
set1 <- RUVSeq::RUVs(x = counts, k =1, scIdx = scIdx, isLog = FALSE)

#get the ruv weights to put into the linear model. n weights = k.
#k=1
RUV_df1 <- set1$W %>% as.data.frame()
RUV_df1$Names <- rownames(RUV_df1)

#Check that the names match
#k=1
RUV_df_rm1 <- RUV_df1[RUV_df1$Names %in% annot$Final_sample_name, ] 
RUV_1 <-  RUV_df_rm1$W_1

#saveRDS(RUV_df_rm1, "data/new/RUV_df_rm1.RDS")
#saveRDS(RUV_1, "data/new/RUV_1.RDS")

#PCA checks
#k=1
prcomp_res_1 <- prcomp(t(set1$normalizedCounts), scale. = FALSE, center = TRUE)
annot_prcomp_res_1 <- prcomp_res_1$x %>% cbind(., annot)

ggplot2::autoplot(prcomp_res_1, data = annot, colour = "Condition", shape = "Time", size =4, x = 1, y = 2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, vjust = -0.5, max.overlaps = 30)+
  ggtitle("RUVs Correction k=1 NormCounts")

Past versions of "RUVs k1-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

ggplot2::autoplot(prcomp_res_1, data = annot, colour = "Condition", shape = "Time", size =4, x=2, y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, vjust = -0.5, max.overlaps = 30)+
  ggtitle("RUVs Correction k=1 NormCounts")

Past versions of "RUVs k1-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#also try by converting these values to log2cpm

RUV_df_rm1_cpm <- cpm(set1$normalizedCounts, log = TRUE)

prcomp_res_1_cpm <- prcomp(t(RUV_df_rm1_cpm), scale. = FALSE, center = TRUE)
annot_prcomp_res_1_cpm <- prcomp_res_1_cpm$x %>% cbind(., annot)

##PC1/2
ggplot2::autoplot(prcomp_res_1_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size = 4,
                  x=1,
                  y=2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=1 log2cpm")

Past versions of "RUVs k1-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###PC2/3
ggplot2::autoplot(prcomp_res_1_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size = 4, 
                  x=2, 
                  y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=1 log2cpm")

Past versions of "RUVs k1-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08
1b8f045	emmapfort	2025-07-03
0b1ffad	emmapfort	2025-07-02

##RUVs with k = 2

#Apply RUVs function from RUVSeq
#"k" will be iteratively adjusted over time depending on your PCA.
set2 <- RUVSeq::RUVs(x = counts, k =2, scIdx = scIdx, isLog = FALSE)

#get the ruv weights to put into the linear model. n weights = k.
#k=2
RUV_df2 <- set2$W %>% as.data.frame()
RUV_df2$Names <- rownames(RUV_df2)

#Check that the names match
#k=2
RUV_df_rm2 <- RUV_df2[RUV_df2$Names %in% annot$Final_sample_name, ] 
RUV_2 <-  RUV_df_rm2$W_2

#PCA checks
#k=2
prcomp_res_2 <- prcomp(t(set2$normalizedCounts), scale. = FALSE, center = TRUE)
annot_prcomp_res_2 <- prcomp_res_2$x %>% cbind(., annot)

##PC1/2
ggplot2::autoplot(prcomp_res_2, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1,
                  y=2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=2 NormCounts")

Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "RUVs k2-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08
1b8f045	emmapfort	2025-07-03
0b1ffad	emmapfort	2025-07-02

###PC2/3
ggplot2::autoplot(prcomp_res_2, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=2 NormCounts")

Warning: ggrepel: 13 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Past versions of "RUVs k2-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now convert this to log2cpm using the normalized counts from set2

RUV_df_rm2_cpm <- cpm(set2$normalizedCounts, log = TRUE)

prcomp_res_2_cpm <- prcomp(t(RUV_df_rm2_cpm), scale. = FALSE, center = TRUE)
annot_prcomp_res_2_cpm <- prcomp_res_2_cpm$x %>% cbind(., annot)

ggplot2::autoplot(prcomp_res_2_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1, 
                  y=2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=2 log2cpm")

Past versions of "RUVs k2-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###PC2/3
ggplot2::autoplot(prcomp_res_2_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=2 log2cpm")

Past versions of "RUVs k2-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#RUVs with k = 3

#Apply RUVs function from RUVSeq
#"k" will be iteratively adjusted over time depending on your PCA.
set3 <- RUVSeq::RUVs(x = counts, k =3, scIdx = scIdx, isLog = FALSE)

#get the ruv weights to put into the linear model. n weights = k.
#k=3
RUV_df3 <- set3$W %>% as.data.frame()
RUV_df3$Names <- rownames(RUV_df3)

#Check that the names match
#k=3
RUV_df_rm3 <- RUV_df3[RUV_df3$Names %in% annot$Final_sample_name, ] 
RUV_3 <-  RUV_df_rm3$W_3

#PCA checks
#k=3
prcomp_res_3 <- prcomp(t(set3$normalizedCounts), scale. = FALSE, center = TRUE)
annot_prcomp_res_3 <- prcomp_res_3$x %>% cbind(., annot)

###PC1/2
ggplot2::autoplot(prcomp_res_3, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1, 
                  y=2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=3 NormCounts")

Past versions of "RUVs k3-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###PC2/3
ggplot2::autoplot(prcomp_res_3, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=3 NormCounts")

Past versions of "RUVs k3-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now convert this to log2cpm using the normalized counts from set3

RUV_df_rm3_cpm <- cpm(set3$normalizedCounts, log = TRUE)

prcomp_res_3_cpm <- prcomp(t(RUV_df_rm3_cpm), scale. = FALSE, center = TRUE)
annot_prcomp_res_3_cpm <- prcomp_res_3_cpm$x %>% cbind(., annot)

##PC1/2
ggplot2::autoplot(prcomp_res_3_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=1, 
                  y=2)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=3 log2cpm")

Past versions of "RUVs k3-3.png"

Version	Author	Date
1b8f045	emmapfort	2025-07-03
14cdab3	emmapfort	2025-07-02
0b1ffad	emmapfort	2025-07-02

###PC2/3
ggplot2::autoplot(prcomp_res_3_cpm, 
                  data = annot, 
                  colour = "Condition", 
                  shape = "Time", 
                  size =4, 
                  x=2, 
                  y=3)+
  theme_bw()+
  scale_color_manual(values=cond_col)+
  ggrepel::geom_text_repel(label= ind_num, 
                           vjust = -0.5, 
                           max.overlaps = 30)+
  ggtitle("RUVs Correction k=3 log2cpm")

Past versions of "RUVs k3-4.png"

Version	Author	Date
1b8f045	emmapfort	2025-07-03
14cdab3	emmapfort	2025-07-02
0b1ffad	emmapfort	2025-07-02

#Plot Spearman Heatmaps for RUVs Normalized Counts Data

#Now that I've put together the PCA plots for both normalized counts and log2cpm
#I want to make these into heatmaps

####RUVs k=1-3
#check to make sure that the column names are correct
dim(RUV_filt_counts)

[1] 14319    42

dim(set1$normalizedCounts)

[1] 14319    42

dim(set2$normalizedCounts)

[1] 14319    42

dim(set3$normalizedCounts)

[1] 14319    42

#take the normalized counts from k=1 and put together a dataframe with the correct columns
normcounts_k0 <- RUV_filt_counts
normcounts_k1 <- set1$normalizedCounts %>% as.data.frame()
#do the same with k=2 and k=3
normcounts_k2 <- set2$normalizedCounts %>% as.data.frame()
normcounts_k3 <- set3$normalizedCounts %>% as.data.frame()

#do the same with the log2cpm conversion
cpm_k0 <- cpm(normcounts_k0, log = TRUE) %>% as.data.frame()
cpm_k1 <- cpm(set1$normalizedCounts, log = TRUE) %>% as.data.frame()
cpm_k2 <- cpm(set2$normalizedCounts, log = TRUE) %>% as.data.frame()
cpm_k3 <- cpm(set3$normalizedCounts, log = TRUE) %>% as.data.frame()

#compute the correlation matrices for RUVs 1-3 with normalized counts
#k=0
cor_matrix_spmn_k0 <- cor(normcounts_k0,
                          y = NULL,
                          use = "everything", 
                          method = "spearman")
#k=1
cor_matrix_spmn_k1 <- cor(normcounts_k1,
                           y = NULL,
                           use = "everything",
                           method = "spearman")

#k=2
cor_matrix_spmn_k2 <- cor(normcounts_k2,
                          y = NULL,
                          use = "everything",
                          method = "spearman")

#k=3
cor_matrix_spmn_k3 <- cor(normcounts_k3,
                          y = NULL,
                          use = "everything",
                          method = "spearman")

#Do the same with the log2cpm converted versions
#k=0
cor_matrix_spmn_k0_cpm <- cor(cpm_k0,
                           y = NULL,
                           use = "everything",
                           method = "spearman")

#k=1
cor_matrix_spmn_k1_cpm <- cor(cpm_k1,
                           y = NULL,
                           use = "everything",
                           method = "spearman")

#k=2
cor_matrix_spmn_k2_cpm <- cor(cpm_k2,
                          y = NULL,
                          use = "everything",
                          method = "spearman")

#k=3
cor_matrix_spmn_k3_cpm <- cor(cpm_k3,
                          y = NULL,
                          use = "everything",
                          method = "spearman")

#extract metadata columns
Individual <- as.character(Metadata$Ind)
Time <- as.character(Metadata$Time)
Treatment <- as.character(Metadata$Drug)

# Define color palettes for annotations
annot_col_cor = list(Treatment = c("DOX" = "#499FBD", 
                               "DMSO" = "#BBBBBC"),
                     Individuals = c("1" = "#003F5C", 
                                     "2" = "#45AE91", 
                                     "3" = "#58209D", 
                                     "4" = "#8B3E9B", 
                                     "5" = "#FF6361", 
                                     "6" = "#BC4169", 
                                     "6R" = "#FF2362"),
                     Timepoints = c("24T" = "#238B45",
                                    "24R" = "#74C476", 
                                    "144R" = "#C7E9C0"))

tx_colors <- c("DOX" = "#499FBD", 
                 "DMSO" = "#BBBBBC")
ind_colors <- c("1" = "red",
                "2" = "orange",
                "3" = "yellow",
                "4" = "green",
                "5" = "blue",
                "6" = "violet",
                "6R" = "purple")
time_colors <- c("24T" = "#238B45",
                 "24R" = "#74C476",
                 "144R" = "#C7E9C0")

# Create annotations
top_annotation <- HeatmapAnnotation(
  Individual = Individual, 
  Time = Time,
  Treatment = Treatment,
  col = list(
    Individual = ind_colors, 
    Time = time_colors,
    Treatment = tx_colors
  )
)

####ANNOTATED HEATMAPS####
###Spearman Heatmap k=0 ####
heatmap_spmn_k0 <- Heatmap(cor_matrix_spmn_k0,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "Filtered Counts no RUVs")

# Draw the heatmap k=0
draw(heatmap_spmn_k0)

Past versions of "RUVs HM Spearman-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=1 ####
heatmap_spmn_k1 <- Heatmap(cor_matrix_spmn_k1,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "Normalized Counts k=1")

# Draw the heatmap k=1
draw(heatmap_spmn_k1)

Past versions of "RUVs HM Spearman-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=2####
heatmap_spmn_k2 <- Heatmap(cor_matrix_spmn_k2,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "Normalized Counts k=2")

# Draw the heatmap k=2
draw(heatmap_spmn_k2)

Past versions of "RUVs HM Spearman-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=3####
heatmap_spmn_k3 <- Heatmap(cor_matrix_spmn_k3,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "Normalized Counts k=3")

# Draw the heatmap k=3
draw(heatmap_spmn_k3)

Past versions of "RUVs HM Spearman-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=0 log2cpm####
heatmap_spmn_k0_cpm <- Heatmap(cor_matrix_spmn_k0_cpm,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "log2cpm of Filtered Counts no RUVs")

# Draw the heatmap k=0 log2cpm
draw(heatmap_spmn_k0_cpm)

Past versions of "RUVs HM Spearman-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=1 log2cpm####
heatmap_spmn_k1_cpm <- Heatmap(cor_matrix_spmn_k1_cpm,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "log2cpm of Normalized Counts k=1")

# Draw the heatmap k=1 log2cpm
draw(heatmap_spmn_k1_cpm)

Past versions of "RUVs HM Spearman-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=2 log2cpm####
heatmap_spmn_k2_cpm <- Heatmap(cor_matrix_spmn_k2_cpm,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "log2cpm of Normalized Counts k=2")

# Draw the heatmap k=2 log2cpm
draw(heatmap_spmn_k2_cpm)

Past versions of "RUVs HM Spearman-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####Spearman Heatmap k=3 log2cpm####
heatmap_spmn_k3_cpm <- Heatmap(cor_matrix_spmn_k3_cpm,
                           name = "Spearman",
                           top_annotation = top_annotation,
                           show_row_names = TRUE,
                           show_column_names = TRUE,
                           cluster_rows = TRUE,
                           cluster_columns = TRUE,
                           border = TRUE, 
                           column_title = "log2cpm of Normalized Counts k=3")

# Draw the heatmap k=3 log2cpm
draw(heatmap_spmn_k3_cpm)

Past versions of "RUVs HM Spearman-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#Perform Differential Expression Analysis with k = 1 RUVs Correction

#same DGEList object as before
dge <- readRDS("data/new/dge_matrix.RDS")

#check normalization factors from TMM normalization of LIBRARIES
dge$samples

                     group lib.size norm.factors
84-1_DOX_24        DOX_24T 23393931    0.9745263
84-1_DMSO_24      DMSO_24T 22853195    0.9565797
84-1_DOX_24+24     DOX_24R 23846995    1.1659432
84-1_DMSO_24+24   DMSO_24R 21299355    0.9649641
84-1_DOX_24+144   DOX_144R 18222568    0.9913625
84-1_DMSO_24+144 DMSO_144R 28115884    0.9653464
87-1_DOX_24        DOX_24T 19935097    1.0526605
87-1_DMSO_24      DMSO_24T 21302879    0.9773889
87-1_DOX_24+24     DOX_24R 25636959    1.0751043
87-1_DMSO_24+24   DMSO_24R 26319662    0.9940323
87-1_DOX_24+144   DOX_144R 23463426    0.9003102
87-1_DMSO_24+144 DMSO_144R 25840938    0.9888449
78-1_DOX_24        DOX_24T 23085807    0.7676077
78-1_DMSO_24      DMSO_24T 25610495    1.0077383
78-1_DOX_24+24     DOX_24R 18083930    1.1682704
78-1_DMSO_24+24   DMSO_24R 24331177    0.9906872
78-1_DOX_24+144   DOX_144R 19754391    0.9941834
78-1_DMSO_24+144 DMSO_144R 22641509    1.0010734
75-1_DOX_24        DOX_24T 20583626    1.0676786
75-1_DMSO_24      DMSO_24T 28166198    1.0031906
75-1_DOX_24+24     DOX_24R 25831427    1.1530208
75-1_DMSO_24+24   DMSO_24R 26081158    1.0058953
75-1_DOX_24+144   DOX_144R 24659898    0.9261599
75-1_DMSO_24+144 DMSO_144R 25412931    0.9703454
17-3_DOX_24        DOX_24T 22518848    0.9766893
17-3_DMSO_24      DMSO_24T 24589534    0.9612345
17-3_DOX_24+24     DOX_24R 24797547    1.1703079
17-3_DMSO_24+24   DMSO_24R 25977536    0.9509690
17-3_DOX_24+144   DOX_144R 27447106    0.9422729
17-3_DMSO_24+144 DMSO_144R 24893583    0.9356377
90-1_DOX_24        DOX_24T 25187428    1.0311957
90-1_DMSO_24      DMSO_24T 25630519    1.0283437
90-1_DOX_24+24     DOX_24R 26138399    1.1183471
90-1_DMSO_24+24   DMSO_24R 24430396    0.9988688
90-1_DOX_24+144   DOX_144R 23323463    0.9496884
90-1_DMSO_24+144 DMSO_144R 25424152    0.9872926

#read in my covariate information RUV_1 dataframe + remove 6R
RUV_df_rm1 <- readRDS("data/new/RUV_df_rm1.RDS")

#filter out 6R for DE analysis
RUV_1_df_filt <- RUV_df_rm1[!grepl("6R$", rownames(RUV_df_rm1)), , drop = FALSE]

Metadata_2$W_1 <- RUV_1_df_filt$W_1

#now ensure that RUV_1 has the right number of cols after removing rep
length(RUV_1_df_filt$W_1)

[1] 36

#36 

#now make this into a list
RUV_1_DE <-  RUV_1_df_filt$W_1

#saveRDS(RUV_1_DE, "data/new/RUV_1_DE.RDS")

#create my design matrix for DE + RUVs covariate k=1
design1 <- model.matrix(~0 + RUV_1_DE + Metadata_2$Condition)
colnames(design1) <- gsub("Metadata_2\\$Condition", "", colnames(design1))

#take care that the matrix automatically sorts cols alphabetically
##currently DMSO144R, DMSO24R, DMSO24T, DOX144R, DOX24R, DOX24T

#run duplicate correlation for individual effect
corfit1 <- duplicateCorrelation(object = dge$counts, design = design1, block = Metadata_2$Ind)

#voom transformation and plot
v1 <- voom(dge, design1, block = Metadata_2$Ind, correlation = corfit1$consensus.correlation, plot = TRUE)

Past versions of "DE RUVs k1-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#fit my linear model
fit1 <- lmFit(v1, design1, block = Metadata_2$Ind, correlation = corfit1$consensus.correlation)

#make my contrast matrix to compare across tx and veh
contrast_matrix_RUV <- makeContrasts(
  V.D24T = DOX_24T - DMSO_24T,
  V.D24R = DOX_24R - DMSO_24R, 
  V.D144R = DOX_144R - DMSO_144R,
  RUV_1_24T = RUV_1_DE - DMSO_24T,
  RUV_1_24R = RUV_1_DE - DMSO_24R,
  RUV_1_144R = RUV_1_DE - DMSO_144R,  
  levels = design1
)

#apply these contrasts to compare DOX to DMSO VEH
fit_RUV <- contrasts.fit(fit1, contrast_matrix_RUV)
fit_RUV <- eBayes(fit_RUV)

#plot the mean-variance trend
plotSA(fit_RUV, main = "Mean-Variance Trend, RUVs k=1")

Past versions of "DE RUVs k1-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#look at the summary of your results
##this tells you the number of DEGs in each condition
results_summary1 <- decideTests(fit_RUV, adjust.method = "BH", p.value = 0.05)

summary(results_summary1)

       V.D24T V.D24R V.D144R RUV_1_24T RUV_1_24R RUV_1_144R
Down     4866   3727     466     13212     13224      13168
NotSig   4899   7107   13659      1014      1002       1058
Up       4554   3485     194        93        93         93

#        V.D24T V.D24R V.D144R RUV_1_24T RUV_1_24R RUV_1_144R
# Down     4866   3727     466     13212     13224      13168
# NotSig   4899   7107   13659      1014      1002       1058
# Up       4554   3485     194        93        93         93

#compare this to my previous DEGs I found
summary(results_summary)

       V.D24T V.D24R V.D144R
Down     4723   3593     359
NotSig   5076   7151   13810
Up       4520   3575     150

#        V.D24T V.D24R V.D144R
# Down     4723   3593     359
# NotSig   5076   7151   13810
# Up       4520   3575     150


#overall, there are more DEGs found after RUVs k=1 correction 
#this was an expected result as it increases tx effect w/ correction

##Generate Toptables RUVs

# Generate Top Table for Specific Comparisons

Toptable_V.D24T_k1 <- topTable(fit = fit_RUV, coef = "V.D24T", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D24T_k1, "data/new/DEGs/Toptable_V.D24T_k1.csv")

Toptable_V.D24R_k1 <- topTable(fit = fit_RUV, coef = "V.D24R", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D24R_k1, "data/new/DEGs/Toptable_V.D24R_k1.csv")

Toptable_V.D144R_k1 <- topTable(fit = fit_RUV, coef = "V.D144R", number = nrow(x), adjust.method = "BH", p.value = 1, sort.by = "none")
#write.csv(Toptable_V.D144R_k1, "data/new/DEGs/Toptable_V.D144R_k1.csv")

# save all of these toptables as R objects
# saveRDS(list(
#   V.D24T_k1 = Toptable_V.D24T_k1,
#   V.D24R_k1 = Toptable_V.D24R_k1,
#   V.D144R_k1 = Toptable_V.D144R_k1
# ), file = "data/new/Toptable_list_RUVk1.RDS")

Toptable_list_RUVk1 <- readRDS("data/new/Toptable_list_RUVk1.RDS")

#################################################################
#this section is commented out since it only needs to run once
#kept the code for posterity

# #I want to add the hgnc symbols to my toptables as well
# ####D24T####
# #load in data
# sample_toptab_24T <- read_csv("data/new/DEGs/Toptable_V.D24T_k1.csv", show_col_types = FALSE)
# # ----------------- Ensure Entrez_ID is Present and in Character Format -----------------
# # Check column names
# print(colnames(sample_toptab_24T))
# # Rename if needed (adjust if the column name is not exactly 'Entrez_ID')
# colnames(sample_toptab_24T)[1] <- "Entrez_ID"
# # Convert Entrez_ID to character
# sample_toptab_24T <- sample_toptab_24T %>%
#   mutate(Entrez_ID = as.character(Entrez_ID))
# # ----------------- Map Entrez_ID to Gene Symbol -----------------
# gene_symbols1 <- AnnotationDbi::select(
#   org.Hs.eg.db,
#   keys = sample_toptab_24T$Entrez_ID,
#   columns = c("SYMBOL"),
#   keytype = "ENTREZID"
# )
# # ----------------- Join Back to Main Data -----------------
# Toptable_RUV_24T <- left_join(sample_toptab_24T, gene_symbols1, by = c("Entrez_ID" = "ENTREZID"))
# Toptable_RUV_24T %>% column_to_rownames(., var = "Entrez_ID")
# # ----------------- Save Annotated Output -----------------
# #write_csv(Toptable_RUV_24T, "data/new/DEGs/Toptable_RUV_24T.csv")
# 
# #now do this again for my other two toptables
# 
# ####24R####
# #load in data
# sample_toptab_24R <- read_csv("data/new/DEGs/Toptable_V.D24R_k1.csv", show_col_types = FALSE)
# # ----------------- Ensure Entrez_ID is Present and in Character Format -----------------
# # Check column names
# print(colnames(sample_toptab_24R))
# # Rename if needed (adjust if the column name is not exactly 'Entrez_ID')
# colnames(sample_toptab_24R)[1] <- "Entrez_ID"
# # Convert Entrez_ID to character
# sample_toptab_24R <- sample_toptab_24R %>%
#   mutate(Entrez_ID = as.character(Entrez_ID))
# # ----------------- Map Entrez_ID to Gene Symbol -----------------
# gene_symbols2 <- AnnotationDbi::select(
#   org.Hs.eg.db,
#   keys = sample_toptab_24R$Entrez_ID,
#   columns = c("SYMBOL"),
#   keytype = "ENTREZID"
# )
# # ----------------- Join Back to Main Data -----------------
# Toptable_RUV_24R <- left_join(sample_toptab_24R, gene_symbols2, by = c("Entrez_ID" = "ENTREZID"))
# Toptable_RUV_24R %>% column_to_rownames(., var = "Entrez_ID")
# # ----------------- Save Annotated Output -----------------
# #I'll make these symbols into rownames later for my volcano plots
# #write_csv(Toptable_RUV_24R, "data/new/DEGs/Toptable_RUV_24R.csv")
# 
# 
# ####D144R####
# #load in data
# sample_toptab_144R <- read_csv("data/new/DEGs/Toptable_V.D144R_k1.csv", show_col_types = FALSE)
# # ----------------- Ensure Entrez_ID is Present and in Character Format -----------------
# # Check column names
# print(colnames(sample_toptab_144R))
# # Rename if needed (adjust if the column name is not exactly 'Entrez_ID')
# colnames(sample_toptab_144R)[1] <- "Entrez_ID"
# # Convert Entrez_ID to character
# sample_toptab_144R <- sample_toptab_144R %>%
#   mutate(Entrez_ID = as.character(Entrez_ID))
# # ----------------- Map Entrez_ID to Gene Symbol -----------------
# gene_symbols3 <- AnnotationDbi::select(
#   org.Hs.eg.db,
#   keys = sample_toptab_144R$Entrez_ID,
#   columns = c("SYMBOL"),
#   keytype = "ENTREZID"
# )
# # ----------------- Join Back to Main Data -----------------
# Toptable_RUV_144R <- left_join(sample_toptab_144R, gene_symbols3, by = c("Entrez_ID" = "ENTREZID"))
# Toptable_RUV_144R %>% column_to_rownames(., var = "Entrez_ID")
# # ----------------- Save Annotated Output -----------------
# #I'll make these symbols into rownames later for my volcano plots
# #write_csv(Toptable_RUV_144R, "data/new/DEGs/Toptable_RUV_144R.csv")

# write.csv(Toptable_RUV_24T, "data/new/DEGs/Toptable_RUV_24T_final.csv")
# write.csv(Toptable_RUV_24R, "data/new/DEGs/Toptable_RUV_24R_final.csv")
# write.csv(Toptable_RUV_144R, "data/new/DEGs/Toptable_RUV_144R_final.csv")

Toptable_RUV_24T <- read.csv("data/new/DEGs/Toptable_RUV_24T_final.csv")
Toptable_RUV_24R <- read.csv("data/new/DEGs/Toptable_RUV_24R_final.csv")
Toptable_RUV_144R <- read.csv("data/new/DEGs/Toptable_RUV_144R_final.csv")



# save all of these toptables as R objects
# saveRDS(list(
#   V.D24T_RUV = Toptable_RUV_24T,
#   V.D24R_RUV = Toptable_RUV_24R,
#   V.D144R_RUV = Toptable_RUV_144R
# ), file = "data/new/Toptable_list_RUVk1_Symbols.RDS")

Toptable_list_RUVk1_symbols <- readRDS("data/new/Toptable_list_RUVk1_Symbols.RDS")

##Volcano Plots of Original DEGs

#make a function to generate volcano plots + add gene numbers
generate_volcano_plot <- function(toptable, title) {
  
  #make significance labels
  toptable$Significance <- "Not Significant"
  toptable$Significance[toptable$logFC > 0 & toptable$adj.P.Val < 0.05] <- "Upregulated"
  toptable$Significance[toptable$logFC < 0 & toptable$adj.P.Val < 0.05] <- "Downregulated"
  
  #add number of genes for each significance label
  upgenes <- toptable %>% filter(Significance == "Upregulated") %>% nrow()
  nsgenes <- toptable %>% filter(Significance == "Not Significant") %>% nrow()
  downgenes <- toptable %>% filter(Significance == "Downregulated") %>% nrow()

  #make legend labels for no of genes
  legend_lab <- c(
    str_c("Upregulated: ", upgenes),
    str_c("Not Significant: ", nsgenes),
    str_c("Downregulated: ", downgenes)
  )
  
  #specify the colors for the legend
  legend_col <- c(
    str_c("Upregulated: " = "blue"),
    str_c("Not Significant: " = "gray"),
    str_c("Downregulated: " = "red")
  )

  #generate volcano plot w/ legend
  ggplot(toptable, aes(x = logFC, 
                       y = -log10(P.Value), 
                       color = Significance)) +
    geom_point(alpha = 0.4, size = 2) + 
    scale_color_manual(values = c("Upregulated" = "blue",
                                  "Not Significant" = "gray",
                                  "Downregulated" = "red"), 
                       labels = legend_lab) +
    xlim(-10, 10) +
    labs(title = title, 
         x = expression(x = "log"[2]*"FC"), 
         y = expression(y = "-log"[10]*"P-value")) +
    theme_bw()+
    guides(color = guide_legend(override.aes = list(color = legend_col)))+
    theme(legend.position = "right", 
          plot.title = element_text(size = rel(1.5), hjust = 0.5),
          axis.title = element_text(size = rel(1.25)))
}

#generate volcano plots across each comparison
volcano_plots <- list(
  "V.D24T" = generate_volcano_plot(Toptable_V.D24T, "Volcano Plot DOX 24hr (adj P-val<0.05)"),
  "V.D24R" = generate_volcano_plot(Toptable_V.D24R, "Volcano Plot DOX 24hr Recovery (adj P-val<0.05)"),
  "V.D144R" = generate_volcano_plot(Toptable_V.D144R, "Volcano Plot DOX 144hr Recovery (adj P-val<0.05)")
)

# Display each volcano plot
for (plot_name in names(volcano_plots)) {
  print(volcano_plots[[plot_name]])
}

Past versions of "Volcano Plots of DEGs Original-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Volcano Plots of DEGs Original-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Volcano Plots of DEGs Original-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Top 5 DEGs after RUVs k=1 Correction

#use your three toptables so I can pull out top 5 genes from each based on adj. p val

top5_D24T_1 <- Toptable_RUV_24T[order(Toptable_RUV_24T$adj.P.Val), ][1:5,] 
top5_D24R_1 <- Toptable_RUV_24R[order(Toptable_RUV_24R$adj.P.Val), ][1:5,] 
top5_D144R_1 <- Toptable_RUV_144R[order(Toptable_RUV_144R$adj.P.Val), ][1:5,]

#now that I've pulled the top 5 DEGs from each, make a list to pull them from my log2cpm data

boxplot1 <- read.csv("data/new/filcpm_final_matrix.csv") %>% 
  as.data.frame()

#Define gene list
#these are the top 5 genes pulled from my toptables
top5_D24T_geneslist_1 <- c(top5_D24T_1$Entrez_ID)
top5_D24R_geneslist_1 <- c(top5_D24R_1$Entrez_ID)
top5_D144R_geneslist_1 <- c(top5_D144R_1$Entrez_ID)
#Add more gene symbols as needed or add more categories

#now pull these from my log2cpm matrix
top5_D24T_genes_1 <- boxplot1[boxplot1$Entrez_ID %in% top5_D24T_geneslist_1,]
dim(top5_D24T_genes_1)

[1]  5 44

#5 genes in 44 cols
top5_D24R_genes_1 <- boxplot1[boxplot1$Entrez_ID %in% top5_D24R_geneslist_1,]
dim(top5_D24R_genes_1)

[1]  5 44

#5 genes in 44 cols
top5_D144R_genes_1 <- boxplot1[boxplot1$Entrez_ID %in% top5_D144R_geneslist_1,]
dim(top5_D144R_genes_1)

[1]  5 44

#5 genes in 44 cols

#Now put in the function I want to use to generate boxplots of genes
#####D24T#####
process_top5_D24T_1 <- function(gene) {
  gene_data <- top5_D24T_genes_1 %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D24T_geneslist_1) {
  gene_data <- process_top5_D24T_1(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm", gene, "top5DEGs D24T RUVs")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "RUV Top5 DEGs-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####D24R#####
process_top5_D24R_1 <- function(gene) {
  gene_data <- top5_D24R_genes_1 %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D24R_geneslist_1) {
  gene_data <- process_top5_D24R_1(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm", gene, "top5DEGs D24R RUVs")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "RUV Top5 DEGs-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-10.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####D144R#####
process_top5_D144R_1 <- function(gene) {
  gene_data <- top5_D144R_genes_1 %>% filter(Entrez_ID == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2cpm") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}


#Generate Boxplots from the above function using our gene list above
for (gene in top5_D144R_geneslist_1) {
  gene_data <- process_top5_D144R_1(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2cpm, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2cpm", gene, "top5DEGs D144R RUVs")) +
    labs(x = "Treatment", y = "log2cpm") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "RUV Top5 DEGs-11.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-12.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-13.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-14.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "RUV Top5 DEGs-15.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##LogFC DEGs RUVs k=1 All Conditions

# Toptable_RUV_24T
# Toptable_RUV_24R
# Toptable_RUV_144R

# Load DEGs Data
DOX_24T_1 <- read.csv("data/new/DEGs/Toptable_RUV_24T_final.csv")
DOX_24R_1 <- read.csv("data/new/DEGs/Toptable_RUV_24R_final.csv")
DOX_144R_1 <- read.csv("data/new/DEGs/Toptable_RUV_144R_final.csv")

#make a list of all of the genes in this set so I can plot the logFC in other sets
D24T_DEGs_1 <- DOX_24T_1$Entrez_ID[DOX_24T_1$adj.P.Val < 0.05]
length(D24T_DEGs_1)

[1] 9420

#9243 genes

D24R_DEGs_1 <- DOX_24R_1$Entrez_ID[DOX_24R_1$adj.P.Val < 0.05]
length(D24R_DEGs_1)

[1] 7212

#7168 genes

D144R_DEGs_1 <- DOX_144R_1$Entrez_ID[DOX_144R_1$adj.P.Val < 0.05]
length(D144R_DEGs_1)

[1] 660

#509 genes

#plot those full gene sets in logFC
D24T_DEGs_1 <- DOX_24T$Entrez_ID[DOX_24T$adj.P.Val < 0.05]
length(D24T_DEGs)

[1] 9243

D24R_DEGs_1 <- DOX_24R$Entrez_ID[DOX_24R$adj.P.Val < 0.05]
length(D24R_DEGs)

[1] 7168

D144R_DEGs_1 <- DOX_144R$Entrez_ID[DOX_144R$adj.P.Val < 0.05]
length(D144R_DEGs)

[1] 509

#now that I have the full list of genes, I want to plot the logFC across conditions


#Combine the toptables I have from pairwise analysis into a single dataframe
d24_toptable_dxr_1 <- Toptable_RUV_24T %>% 
  mutate(Time = "24")

d24r_toptable_dxr_1 <- Toptable_RUV_24R %>% 
  mutate(Time = "24R")

d144r_toptable_dxr_1 <- Toptable_RUV_144R %>% 
  mutate(Time = "144R")

combined_toptables_dxr_RUV <- bind_rows(
  d24_toptable_dxr_1,
  d24r_toptable_dxr_1,
  d144r_toptable_dxr_1)

#Filter the data based on each motif
filt_toptable_dxr_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(Entrez_ID  %in% D24T_DEGs_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC D24T DEGs Across Conditions RUVs")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#now do the same with the other conditions

filt_toptable_dxr_24r_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(Entrez_ID  %in% D24R_DEGs_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC D24R DEGs Across Conditions RUVs")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#D144R

filt_toptable_dxr_144r_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(Entrez_ID  %in% D144R_DEGs_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC D144R DEGs Across Conditions RUVs")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#now put the names of these graphs to print them
filt_toptable_dxr_RUV

Past versions of "RUV logFC DEGs all Conditions-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_dxr_24r_RUV

Past versions of "RUV logFC DEGs all Conditions-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_dxr_144r_RUV

Past versions of "RUV logFC DEGs all Conditions-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Volcano Plots of RUVs Corrected Data k=1

#make a function to generate volcano plots + add gene numbers
#ensure the gene symbols are in a col so I can plot names of top 15
generate_volcano_plot_RUV <- function(toptable, title) {
  
  #make significance labels
  toptable$Significance <- "Not Significant"
  toptable$Significance[toptable$logFC > 0 & toptable$adj.P.Val < 0.05] <- "Upregulated"
  toptable$Significance[toptable$logFC < 0 & toptable$adj.P.Val < 0.05] <- "Downregulated"
  
  #add number of genes for each significance label
  upgenes <- toptable %>% filter(Significance == "Upregulated") %>% nrow()
  nsgenes <- toptable %>% filter(Significance == "Not Significant") %>% nrow()
  downgenes <- toptable %>% filter(Significance == "Downregulated") %>% nrow()

  #make legend labels for no of genes
  legend_lab <- c(
    str_c("Upregulated: ", upgenes),
    str_c("Not Significant: ", nsgenes),
    str_c("Downregulated: ", downgenes)
  )
  
  #specify the colors for the legend
  legend_col <- c(
    str_c("Upregulated: " = "blue"),
    str_c("Not Significant: " = "gray"),
    str_c("Downregulated: " = "red")
  )
  
  #add the top 15 genes by adj. p value
  top_genes <- toptable %>%
    filter(!is.na(SYMBOL)) %>%
    arrange(adj.P.Val) %>%
    slice_head(n = 15)
  
  #generate volcano plot w/ legend
  ggplot(toptable, aes(x = logFC, 
                       y = -log10(P.Value), 
                       color = Significance)) +
    geom_point(alpha = 0.4, size = 2) + 
    scale_color_manual(values = c("Upregulated" = "blue",
                                  "Not Significant" = "gray",
                                  "Downregulated" = "red"), 
                       labels = legend_lab) +
    xlim(-10, 10) +
    labs(title = title, 
         x = expression(x = "log"[2]*"FC"), 
         y = expression(y = "-log"[10]*"P-value")) +
    theme_bw()+
    guides(color = guide_legend(override.aes = list(color = legend_col)))+
    theme(legend.position = "right", 
          plot.title = element_text(size = rel(1.5), hjust = 0.5),
          axis.title = element_text(size = rel(1.25)))
}

#generate volcano plots across each comparison
volcano_plots_RUV <- list(
  "V.D24T_RUV" = generate_volcano_plot(Toptable_RUV_24T, "DOX 24T RUVs k=1 (adj P-val<0.05)"),
  "V.D24R_RUV" = generate_volcano_plot(Toptable_RUV_24R, "DOX 24R RUVs k=1 (adj P-val<0.05)"),
  "V.D144R_RUV" = generate_volcano_plot(Toptable_RUV_144R, "DOX 144R RUVs k=1 (adj P-val<0.05)")
)

# Display each volcano plot
for (plot_name in names(volcano_plots_RUV)) {
  print(volcano_plots_RUV[[plot_name]])
}

Past versions of "Volcano Plots RUVs Corrected k1-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Volcano Plots RUVs Corrected k1-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "Volcano Plots RUVs Corrected k1-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Plot DNA Damage Response Genes (DDR) with Original Data

#DDR Gene Expression Heatmap — DOX Over Recovery Time (68 genes, with categories)

# Load libraries
# library(circlize)
# library(grid)
# library(reshape2)

# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T <- load_deg("data/new/DEGs/Toptable_V.D24T.csv")
DOX_24R <- load_deg("data/new/DEGs/Toptable_V.D24R.csv")
DOX_144R <- load_deg("data/new/DEGs/Toptable_V.D144R.csv")

# Final Entrez IDs and categories (68 genes)
entrez_category_DDR <- tribble(
  ~ENTREZID, ~Category,
  317, "Apoptosis", 355, "Apoptosis", 581, "Apoptosis", 637, "Apoptosis",
  836, "Apoptosis", 841, "Apoptosis", 842, "Apoptosis", 27113, "Apoptosis",
  5366, "Apoptosis", 54205, "Apoptosis", 55367, "Apoptosis", 8795, "Apoptosis",
  1026, "Cell Cycle / Checkpoint", 1027, "Cell Cycle / Checkpoint", 595, "Cell Cycle / Checkpoint",
  894, "Cell Cycle / Checkpoint", 896, "Cell Cycle / Checkpoint", 898, "Cell Cycle / Checkpoint",
  9133, "Cell Cycle / Checkpoint", 9134, "Cell Cycle / Checkpoint", 891, "Cell Cycle / Checkpoint",
  983, "Cell Cycle / Checkpoint", 1017, "Cell Cycle / Checkpoint", 1019, "Cell Cycle / Checkpoint",
  1020, "Cell Cycle / Checkpoint", 1021, "Cell Cycle / Checkpoint", 993, "Cell Cycle / Checkpoint",
  995, "Cell Cycle / Checkpoint", 1869, "Cell Cycle / Checkpoint", 4609, "Cell Cycle / Checkpoint",
  5925, "Cell Cycle / Checkpoint", 9874, "Cell Cycle / Checkpoint", 11011, "Cell Cycle / Checkpoint",
  1385, "Cell Cycle / Checkpoint",
  472, "Damage Sensors / Signal Transducers", 545, "Damage Sensors / Signal Transducers",
  5591, "Damage Sensors / Signal Transducers", 5810, "Damage Sensors / Signal Transducers",
  5883, "Damage Sensors / Signal Transducers", 5884, "Damage Sensors / Signal Transducers",
  6118, "Damage Sensors / Signal Transducers", 4361, "Damage Sensors / Signal Transducers",
  10111, "Damage Sensors / Signal Transducers", 4683, "Damage Sensors / Signal Transducers",
  84126, "Damage Sensors / Signal Transducers", 3014, "Damage Sensors / Signal Transducers",
  672, "DNA Repair", 2177, "DNA Repair", 5888, "DNA Repair", 5893, "DNA Repair",
  1647, "DNA Repair", 4616, "DNA Repair", 10912, "DNA Repair", 1111, "DNA Repair",
  11200, "DNA Repair", 1643, "DNA Repair", 8243, "DNA Repair", 5981, "DNA Repair",
  7157, "p53 Regulators / Targets", 4193, "p53 Regulators / Targets", 5371, "p53 Regulators / Targets",
  27244, "p53 Regulators / Targets", 50484, "p53 Regulators / Targets",
  5916, "DOX Cardiotoxicity", 7799, "DOX Cardiotoxicity", 4292, "DOX Cardiotoxicity",
  207, "Miscellaneous / Broad", 25, "Miscellaneous / Broad"
)

entrez_ids_DDR <- entrez_category_DDR$ENTREZID

# Extract relevant DEG values
extract_data_DDR <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_DDR) %>%
    mutate(
      Gene = mapIds(org.Hs.eg.db, as.character(Entrez_ID),
                    column = "SYMBOL", keytype = "ENTREZID", multiVals = "first"),
      Condition = name,
      Signif = ifelse(adj.P.Val < 0.05, "*", "")
    )
}

# DEG list
deg_list <- list("DOX_24T" = DOX_24T, 
                 "DOX_24R" = DOX_24R, 
                 "DOX_144R" = DOX_144R
)

# Combine all DEGs and annotate
all_data_DDR <- bind_rows(mapply(extract_data_DDR, deg_list, names(deg_list), SIMPLIFY = FALSE)) %>%
  left_join(entrez_category_DDR, by = c("Entrez_ID" = "ENTREZID"))

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

# Create matrices
logFC_matddr <- acast(all_data_DDR, Gene ~ Condition, value.var = "logFC")
signif_matddr <- acast(all_data_DDR, Gene ~ Condition, value.var = "Signif")

# Set desired order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_DDR <- logFC_matddr[, desired_order, drop = FALSE]
signif_mat_DDR <- signif_matddr[, desired_order, drop = FALSE]

# Column annotation
meta_DDR <- str_split_fixed(colnames(logFC_mat_DDR), "_", 2)
col_annot <- HeatmapAnnotation(
  Drug = meta_DDR[, 1],
  Time = meta_DDR[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(1, 1, 1), "cm")
)

# Row annotation
gene_order_df_DDR <- all_data_DDR %>%
  distinct(Gene, Category) %>%
  arrange(factor(Category, levels = sort(unique(entrez_category_DDR$Category))), Gene)

ordered_genes_DDR <- gene_order_df_DDR$Gene
logFC_mat_DDR <- logFC_mat_DDR[ordered_genes_DDR, ]
signif_mat_DDR <- signif_mat_DDR[ordered_genes_DDR, ]

category_colors_DDR <- structure(
  c("darkorange", "steelblue", "darkgreen", "firebrick", "gold", "mediumpurple", "gray60"),
  names = sort(unique(entrez_category_DDR$Category))
)

ha_left_DDR <- rowAnnotation(
  Category = gene_order_df_DDR$Category,
  col = list(Category = category_colors_DDR),
  annotation_name_side = "top"
)

# Final Heatmap
Heatmap(logFC_mat_DDR,
        name = "logFC",
        top_annotation = col_annot,
        left_annotation = ha_left_DDR,
        cluster_columns = FALSE,
        cluster_rows = FALSE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        row_names_gp = gpar(fontsize = 10),
        column_title = "DDR Gene Expression Response (n = 68)\n DOX Recovery",
        column_title_gp = gpar(fontsize = 14, fontface = "bold"),
        cell_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_DDR[i, j], x, y, gp = gpar(fontsize = 9))
        }
)

Past versions of "DDR Genes logFC-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Plot DOX Cardiotox Genes logFC HM Original Data

#plot a list of 29 functionally validated DIC genes
# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T <- load_deg("data/new/DEGs/Toptable_V.D24T.csv")
DOX_24R <- load_deg("data/new/DEGs/Toptable_V.D24R.csv")
DOX_144R <- load_deg("data/new/DEGs/Toptable_V.D144R.csv")

#the data I have is in hgnc_symbols, I want to convert this to entrez_id like my df
DIC_genes <- tribble(
  ~SYMBOL, ~Category,
  "CAT", "ROS Generation / Handling",
  "CBR1", "ROS Generation / Handling",
  "CBR3", "ROS Generation / Handling",
  "ERBB2", "ROS Generation / Handling",
  "GPX3", "ROS Generation / Handling",
  "GSTM1", "ROS Generation / Handling",
  "GSTP", "ROS Generation / Handling",
  "HAS3", "ROS Generation / Handling",
  "NOS3", "ROS Generation / Handling",
  "PLCE1", "ROS Generation / Handling",
  "RAC2", "ROS Generation / Handling",
  "SPG7", "ROS Generation / Handling",
  "PRDM2", "DNA Damage", 
  "MLH1", "DNA Damage",
  "RARG", "DNA Damage",
  "HFE", "Iron Uptake & Homeostasis",
  "SLC22A17", "DOX Uptake",
  "SLC28A1", "DOX Uptake",
  "SLC28A3", "DOX Uptake",
  "ABCB4", "DOX Efflux",
  "ABCC2", "DOX Efflux",
  "ABCC5", "DOX Efflux", 
  "ABCC9", "DOX Efflux",
  "ABCC10", "DOX Efflux",
  "CELF4", "Calcium Handling",
  "MYH7", "Calcium Handling",
  "CYP2J2", "Cardiac Electrical Activity",
  "RIN3", "Cardiac Electrical Activity",
  "ZFN521", "Cardiac Electrical Activity")

gene_df_DIC <- tibble(HGNC = DIC_genes)


gene_df_DIC <- gene_df_DIC %>% 
  mutate(Entrez_ID = mapIds(org.Hs.eg.db,
                            keys = DIC_genes$SYMBOL,
                            column = "ENTREZID", 
                            keytype = "SYMBOL", 
                            multiVals = "first")) %>% 
  unnest_wider(HGNC) %>% 
  mutate(Entrez_ID = as.character(Entrez_ID))

'select()' returned 1:1 mapping between keys and columns

#now I've put together a dataframe with the HGNC, Category, and Entrez_ID
#plus I've ensured that Entrez_ID is a character for later joining

entrez_ids_DIC <- gene_df_DIC$Entrez_ID

# saveRDS(entrez_ids_DIC, "data/new/RUV/DIC_genes_entrezid.RDS")

# Extract relevant DEG values
extract_data_DIC <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_DIC) %>%
    mutate(
      Gene = mapIds(org.Hs.eg.db, as.character(Entrez_ID),
                    column = "SYMBOL", keytype = "ENTREZID", multiVals = "first"),
      Condition = name,
      Signif = ifelse(adj.P.Val < 0.05, "*", "")
    )
}

# DEG list
deg_list <- list("DOX_24T" = DOX_24T, 
                 "DOX_24R" = DOX_24R, 
                 "DOX_144R" = DOX_144R
)

# Combine all DEGs and annotate
all_data_DIC <- bind_rows(mapply(extract_data_DIC, 
                             deg_list, 
                             names(deg_list), 
                             SIMPLIFY = FALSE)) %>%
  mutate(Entrez_ID = as.character(Entrez_ID)) %>% 
  left_join(gene_df_DIC, 
            by = "Entrez_ID")

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

#I've also made sure here that Entrez_ID is a character and not an integer

# Create matrices
logFC_matdic <- acast(all_data_DIC, Gene ~ Condition, value.var = "logFC")
signif_matdic <- acast(all_data_DIC, Gene ~ Condition, value.var = "Signif")

# Set desired order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_DIC <- logFC_matdic[, desired_order, drop = FALSE]
signif_mat_DIC <- signif_matdic[, desired_order, drop = FALSE]

# Column annotation
meta_DIC <- str_split_fixed(colnames(logFC_mat_DIC), "_", 3)
meta_DIC <- str_split_fixed(colnames(logFC_mat_DIC), "_", 2)
col_annot <- HeatmapAnnotation(
  Drug = meta_DIC[, 1],
  Time = meta_DIC[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(2, 2, 2), "cm")
)
#for this I can leave off the DMSO as it's already from a pairwise comparison

#make an extra object with my category order as well
category_order_DIC <- c(
  "ROS Generation / Handling",
  "DNA Damage",
  "Calcium Handling",
  "DOX Uptake",
  "Iron Uptake & Homeostasis",
  "DOX Efflux",
  "Cardiac Electrical Activity"
)

# Row annotation
gene_order_df_DIC <- all_data_DIC %>%
  distinct(Gene, Category) %>%
  mutate(Category = factor(Category, levels = category_order_DIC)) %>% 
  arrange(Category, Gene)

ordered_genes_DIC <- gene_order_df_DIC$Gene
logFC_mat_DIC <- logFC_mat_DIC[ordered_genes_DIC, ]
signif_mat_DIC <- signif_mat_DIC[ordered_genes_DIC, ]

#add in your colors for each category
 category_colors_DIC <- structure(
  c("darkorange", "steelblue", "darkgreen", "firebrick", "gold", "mediumpurple", "gray60"),
  names = category_order_DIC
)

ha_left_DIC <- rowAnnotation(
  Category = gene_order_df_DIC$Category,
  col = list(Category = category_colors_DIC),
  annotation_name_side = "top"
)

# Draw heatmap
Heatmap(logFC_mat_DIC,
        name = "logFC",
        top_annotation = col_annot,
        left_annotation = ha_left_DIC,
        cluster_columns = FALSE,
        cluster_rows = FALSE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        cell_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_DIC[i, j], x, y, gp = gpar(fontsize = 9))
        },
        column_title = "DIC Genes Expression (n=29)\nDOX Recovery",
        column_title_gp = gpar(fontsize = 14, fontface = "bold")
)

Past versions of "DIC Genes logFC HM noRUVs-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Plot p53 Target Genes logFC HM Original Data

# Load libraries
library(tidyverse)
library(ComplexHeatmap)
library(circlize)
library(grid)
library(org.Hs.eg.db)
library(reshape2)

# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T <- load_deg("data/new/DEGs/Toptable_V.D24T.csv")
DOX_24R <- load_deg("data/new/DEGs/Toptable_V.D24R.csv")
DOX_144R <- load_deg("data/new/DEGs/Toptable_V.D144R.csv")

#P53 target Entrez_ID
entrez_ids_p53 <- c(1026,50484,4193,9766,9518,7832,1643,1647,1263,57103,51065,8795,51499,64393,581,
                5228,5429,8493,55959,7508,64782,282991,355,53836,4814,10769,9050,27244,9540,94241,
                26154,57763,900,26999,55332,26263,23479,23612,29950,9618,10346,8824,134147,55294,
                22824,4254,6560,467,27113,60492,8444,60401,1969,220965,2232,3976,55191,84284,93129,
                5564,7803,83667,7779,132671,7039,51768,137695,93134,7633,10973,340485,307,27350,
                23245,3732,29965,1363,1435,196513,8507,8061,2517,51278,53354,54858,23228,5366,5912,
                6236,51222,26152,59,1907,50650,91012,780,9249,11072,144455,64787,116151,27165,2876,
                57822,55733,57722,121457,375449,85377,4851,5875,127544,29901,84958,8797,8793,441631,
                220001,54541,5889,5054,25816,25987,5111,98,317,598,604,10904,1294,80315,53944,
                1606,2770,3628,3675,3985,4035,4163,84552,29085,55367,5371,5791,54884,5980,8794,
                1462,50808,220,583,694,1056,9076,10978,54677,1612,55040,114907,2274,127707,4000,
                8079,4646,4747,27445,5143,80055,79156,5360,5364,23654,5565,5613,5625,10076,56963,
                6004,390,255488,6326,6330,23513,7869,283130,204962,83959,6548,6774,9263,10228,
                22954,10475,85363,494514,10142,79714,1006,8446,9648,79828,5507,55240,63874,25841,
                9289,84883,154810,51321,421,8553,655,119032,84280,10950,824,839,57828,857,8812,
                8837,94027,113189,22837,132864,10898,3300,81704,1847,1849,1947,9538,24139,5168,
                147965,115548,9873,23768,2632,2817,3280,3265,23308,3490,51477,182,3856,8844,144811,
                9404,4043,9848,2872,23041,740,343263,4638,26509,4792,22861,57523,55214,80025,164091,
                57060,64065,51090,5453,8496,333926,55671,5900,55544,23179,8601,389,6223,55800,6385,
                4088,6643,122809,257397,285343,7011,54790,374618,55362,51754,7157,9537,22906,7205,
                80705,219699,55245,83719,7748,25946,118738)

# p53_genes <- saveRDS(entrez_ids_p53, "data/new/RUV/p53_genelist_entrezid.RDS")

# Function to extract relevant data
extract_data_p53 <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_p53) %>%
    mutate(Gene = mapIds(org.Hs.eg.db, as.character(Entrez_ID),
                         column = "SYMBOL", keytype = "ENTREZID", multiVals = "first"),
           Condition = name,
           Signif = ifelse(adj.P.Val < 0.05, "*", ""))
}

# Collect all data
# DEG list
deg_list <- list("DOX_24T" = DOX_24T, 
                 "DOX_24R" = DOX_24R, 
                 "DOX_144R" = DOX_144R
)

# Combine all DEGs and annotate
all_data_p53 <- bind_rows(mapply(extract_data_p53, deg_list, names(deg_list), SIMPLIFY = FALSE)) 

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

#unnecessary to join again as there are not categories on this list of entrezids
# %>%
#   left_join(entrez_ids, by = c("Entrez_ID" = "ENTREZID"))

# Create matrices
logFC_mat53 <- acast(all_data_p53, Gene ~ Condition, value.var = "logFC")
signif_mat53 <- acast(all_data_p53, Gene ~ Condition, value.var = "Signif")

# Desired column order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_p53 <- logFC_mat53[, desired_order]
signif_mat_p53 <- signif_mat53[, desired_order]

# Column annotation
meta_p53 <- str_split_fixed(colnames(logFC_mat_p53), "_", 3)
meta_p53 <- str_split_fixed(colnames(logFC_mat_p53), "_", 2)
col_annot <- HeatmapAnnotation(
  Drug = meta_p53[, 1],
  Time = meta_p53[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(1, 1, 1), "cm")
)

# Draw heatmap
Heatmap(logFC_mat_p53,
        name = "logFC",
        top_annotation = col_annot,
        cluster_columns = FALSE,
        cluster_rows = TRUE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        layer_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_p53[cbind(i, j)], x, y, gp = gpar(fontsize = 9))
        },
        column_title = "P53 Target Genes Expression\nDOX Recovery",
        column_title_gp = gpar(fontsize = 14, fontface = "bold")
)

Past versions of "p53 Target Genes logFC HM-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Create a Venn Diagram of DEGs from Original DEA

#plot a venn diagram with all of your conditions from your toptables

# Load DEGs Data
DOX_24T <- read.csv("data/new/DEGs/Toptable_V.D24T.csv")
DOX_24R <- read.csv("data/new/DEGs/Toptable_V.D24R.csv")
DOX_144R <- read.csv("data/new/DEGs/Toptable_V.D144R.csv")

# Extract Significant DEGs
DEG1 <- DOX_24T$Entrez_ID[DOX_24T$adj.P.Val < 0.05]
DEG2 <- DOX_24R$Entrez_ID[DOX_24R$adj.P.Val < 0.05]
DEG3 <- DOX_144R$Entrez_ID[DOX_144R$adj.P.Val < 0.05]


venntest <- list(DEG1, DEG2, DEG3)
ggVennDiagram(
  venntest,
  category.names = c("DOX_24T", "DOX_24R", "DOX_144R")
) + ggtitle("DXR Specific and Shared DEGs")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Overlap of DEGs Original-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#Now that I've made my venn diagram, I want to compare these DEGs
#set 1 : 4362 DOX24T specific genes
#set2 : 4362 + 4550 + 50 + 272 genes shared across DOX24T (all genes)
#how many of these are downregulated and how many are upregulated?

# Extract Significant DEGs
# Create a list of DEGs for each sample

# Example gene sets

DEG1 <- DOX_24T$Entrez_ID[DOX_24T$adj.P.Val < 0.05]
DEG2 <- DOX_24R$Entrez_ID[DOX_24R$adj.P.Val < 0.05]
DEG3 <- DOX_144R$Entrez_ID[DOX_144R$adj.P.Val < 0.05]

#try and use the VennDetail package to extract the genes from each condition
#Set 1 - DOX_24T only genes
#Set 2 - DOX_24T shared genes
plot.new()
venn_test <- venndetail(venntest)
plot(venn_test)

Past versions of "Overlap of DEGs Original-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

detail(venn_test)

=== Here is the detail of Venndiagram ===
Total results:  11612 x 2 
Total sets is: 7 
  Subset Detail
1 Shared 643837
2 Shared   1870
3 Shared  84958
4 Shared   2537
5 Shared 192670
6 Shared   1298
... with 11606 more rows ...

#now that I have the genes subsetted by condition, I can pull out the genes I want to look at

venn_DOX_24T <- getSet(object = venn_test, subset = c("Group 1"))

Warning: `filter_()` was deprecated in dplyr 0.7.0.
ℹ Please use `filter()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the VennDetail package.
  Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
generated.

dim(venn_DOX_24T)

[1] 4362    2

#4362 genes in DOX_24T only

venn_DOX_shared <- getSet(object = venn_test, subset = c("Shared", "Group 1", "Group 1_Group 2", "Group 1_Group 3"))
dim(venn_DOX_shared)

[1] 9243    2

#total of 9243 genes:
  #4559 DOX_24T only 
  #272 shared all
  #50 DOX_24T + DOX_144R
  #4362 DOX_24T + DOX_24R

venn_DOX144R_shared <- getSet(object = venn_test, subset = c("Shared", "Group 3", "Group 2_Group 3", "Group 1_Group 3"))
dim(venn_DOX144R_shared)

[1] 509   2

#total of 509 genes:
 #272 shared all
 #32 DOX144R Specific
 #50 DOX24T + DOX144R
 #155 DOX24R + DOX144R

#now I can look at these sets to see which ones are up and down regulated in each
#after that, run GO analysis
venn_shared_DEGs <- venn_DOX_shared %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

venn_sharedD144R_DEGs <- venn_DOX144R_shared %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

venn_DOX24T_DEGs <- venn_DOX_24T %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")


#pull these genes out of my DEG matrix with logFC
DOX_24T_DEGs <- Toptable_list$V.D24T[row.names(venn_DOX24T_DEGs),]
DOX_24T_shared_DEGs <- Toptable_list$V.D24T[row.names(venn_shared_DEGs),]
DOX_144R_shared_DEGs <- Toptable_list$V.D144R[row.names(venn_sharedD144R_DEGs),]
#I want to go ahead and do this for every condition so I can see the genes in there
#I also want to filter these by their logFC being up or down for GO/KEGG

DOX24T_DEGs_GO <- DOX_24T_DEGs %>% 
  dplyr::filter(., adj.P.Val < 0.05)

DOX24T_DEGs_GO_up <- DOX24T_DEGs_GO %>% 
  dplyr::filter(., logFC > 0)  %>% 
  rownames_to_column(., var = "entrezgene_ID") %>% 
  dplyr::select("entrezgene_ID")
#has 4029 genes

DOX24T_DEGs_GO_down <- DOX24T_DEGs_GO %>% 
  dplyr::filter(., logFC < 0)  %>% 
  rownames_to_column(., var = "entrezgene_ID") %>% 
  dplyr::select("entrezgene_ID")
#has 4305 genes

#shared genes venn diagram
DOX24Tshare_DEGs_GO <- DOX_24T_shared_DEGs %>% 
  dplyr::filter(., adj.P.Val < 0.05) 

DOX24T_share_DEGs_GO_plot <- DOX24Tshare_DEGs_GO %>% 
  rownames_to_column(., var = "Entrez_ID") %>% 
  dplyr::select("Entrez_ID")

DOX24Tshare_DEGs_GO_up <- DOX24Tshare_DEGs_GO %>% 
  dplyr::filter(., logFC > 0)  %>% 
  rownames_to_column(., var = "entrezgene_ID") %>% 
  dplyr::select("entrezgene_ID")
#has 4731 genes

DOX24Tshare_DEGs_GO_down <- DOX24Tshare_DEGs_GO %>% 
  dplyr::filter(., logFC < 0)  %>% 
  rownames_to_column(., var = "entrezgene_ID") %>% 
  dplyr::select("entrezgene_ID")

DOX144Rshare_DEGs_GO <- DOX_144R_shared_DEGs %>% 
  dplyr::filter(., adj.P.Val < 0.05)

DOX144Rshare_DEGs_GO_plot <- DOX144Rshare_DEGs_GO %>% 
  rownames_to_column(., var = "Entrez_ID") %>% 
  dplyr::select("Entrez_ID")


#now go ahead and do this for each condition as well

#DOX24T
venn_DOX_24T <- getSet(object = venn_test, subset = c("Group 1"))
dim(venn_DOX_24T)

[1] 4362    2

#4362 genes in DOX_24T only

venn_DOX24T_DEGs <- venn_DOX_24T %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_24T_DEGs <- Toptable_list$V.D24T[row.names(venn_DOX24T_DEGs),]

DOX24T_DEGs_GO <- DOX_24T_DEGs %>% 
  rownames_to_column(., var = "Entrez_ID") %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")

#DOX24R
venn_DOX_24R <- getSet(object = venn_test, subset = c("Group 2"))
dim(venn_DOX_24R)

[1] 2182    2

#2182 genes in DOX_24R only

venn_DOX24R_DEGs <- venn_DOX_24R %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_24R_DEGs <- Toptable_list$V.D24R[row.names(venn_DOX24R_DEGs),]

DOX24R_DEGs_GO <- DOX_24R_DEGs %>% 
  rownames_to_column(., var = "Entrez_ID") %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")


#DOX144R
venn_DOX_144R <- getSet(object = venn_test, subset = c("Group 3"))
dim(venn_DOX_144R)

[1] 32  2

#32 genes in DOX_144R only

venn_DOX144R_DEGs <- venn_DOX_144R %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_144R_DEGs <- Toptable_list$V.D144R[row.names(venn_DOX144R_DEGs),]

DOX144R_DEGs_GO <- DOX_144R_DEGs %>% 
  rownames_to_column(., var = "Entrez_ID") %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")

#this set doesn't yield a GO/KEGG plot as there are too few genes
#instead, I pulled all genes associated with DOX144R

##Venn Diagrams of DEG Overlap after RUVs Correction k=1

#plot a venn diagram with all of your conditions from your toptables

# Load DEGs Data
DOX_24T_1 <- read.csv("data/new/DEGs/TTBL_RUV_24T_OLD.csv")
DOX_24R_1 <- read.csv("data/new/DEGs/TTBL_RUV_24R_OLD.csv")
DOX_144R_1 <- read.csv("data/new/DEGs/TTBL_RUV_144R_OLD.csv")

# Extract Significant DEGs
DEG1_RUV <- DOX_24T_1$Entrez_ID[DOX_24T_1$adj.P.Val < 0.05]
DEG2_RUV <- DOX_24R_1$Entrez_ID[DOX_24R_1$adj.P.Val < 0.05]
DEG3_RUV <- DOX_144R_1$Entrez_ID[DOX_144R_1$adj.P.Val < 0.05]

venntest_RUV <- list(DEG1_RUV, DEG2_RUV, DEG3_RUV)
ggVennDiagram(
  venntest_RUV,
  category.names = c("DOX_24T", "DOX_24R", "DOX_144R")
) + ggtitle("DXR Specific and Shared DEGs RUVs")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "RUVs Overlap of DEGs-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#try and use the VennDetail package to extract the genes from each condition
#Set 1 - DOX_24T only genes
#Set 2 - DOX_24T shared genes
#Set 3 - DOX_144R shared genes
plot.new()
venn_test_RUV <- venndetail(venntest_RUV)
plot(venn_test_RUV)

Past versions of "RUVs Overlap of DEGs-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

detail(venn_test_RUV)

=== Here is the detail of Venndiagram ===
Total results:  11760 x 2 
Total sets is: 7 
  Subset Detail
1 Shared 643837
2 Shared  60672
3 Shared  55450
4 Shared   1870
5 Shared  57822
6 Shared  84958
... with 11754 more rows ...

#now that I have the genes subsetted by condition, I can pull out the genes I want to look at

venn_DOX_24T_RUV <- getSet(object = venn_test_RUV, subset = c("Group 1"))
dim(venn_DOX_24T_RUV)

[1] 4411    2

#4411 genes in DOX_24T only

venn_DOX_shared_RUV <- getSet(object = venn_test_RUV, subset = c("Shared", "Group 1_Group 2", "Group 1_Group 3"))
dim(venn_DOX_shared_RUV)

[1] 5009    2

#total of 5009 genes in this set which does not include D24T specific genes

venn_DOX144R_shared_RUV <- getSet(object = venn_test_RUV, subset = c("Shared", "Group 3", "Group 2_Group 3", "Group 1_Group 3"))
dim(venn_DOX144R_shared_RUV)

[1] 660   2

#total of 660 genes: (original 509)
 #342 shared all
 #32 DOX144R Specific
 #85 DOX24T + DOX144R
 #181 DOX24R + DOX144R

#after that, run GO analysis
venn_shared_DEGs_RUV <- venn_DOX_shared_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

venn_DOX24T_DEGs_RUV <- venn_DOX_24T_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

venn_sharedD144R_DEGs_RUV <- venn_DOX144R_shared_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_24T_DEGs_RUV <-
  Toptable_list_RUVk1_symbols$V.D24T_RUV[row.names(venn_DOX24T_DEGs_RUV),]
DOX_24T_shared_DEGs_RUV <- 
  Toptable_list_RUVk1_symbols$V.D24T_RUV[row.names(venn_shared_DEGs_RUV),]
DOX_144R_shared_DEGs_RUV <- 
  Toptable_list_RUVk1_symbols$V.D144R_RUV[row.names(venn_sharedD144R_DEGs_RUV),]

#next, make the vectors that I need for plotting after cutting off by adj. p value < 0.05
DOX24T_DEGs_GO_RUV <- DOX_24T_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05)

#shared D24T genes venn diagram
DOX24Tshare_DEGs_GO_RUV <- DOX_24T_shared_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05) 

DOX24T_share_DEGs_GO_plot_RUV <- DOX24Tshare_DEGs_GO_RUV %>% 
  dplyr::select("Entrez_ID")

#shared D144R genes venn diagram

DOX144Rshare_DEGs_GO_RUV <- DOX_144R_shared_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05)

DOX144Rshare_DEGs_GO_plot_RUV <- DOX144Rshare_DEGs_GO_RUV %>% 
  dplyr::select("Entrez_ID")

#now go ahead and do this for each condition as well

#DOX24T
venn_DOX_24T_RUV <- getSet(object = venn_test_RUV, subset = c("Group 1"))
dim(venn_DOX_24T_RUV)

[1] 4411    2

#4411 genes in DOX_24T only

venn_DOX24T_DEGs_RUV <- venn_DOX_24T_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_24T_DEGs_RUV <- Toptable_list_RUVk1_symbols$V.D24T_RUV[row.names(venn_DOX24T_DEGs_RUV),]

DOX24T_DEGs_GO_RUV <- DOX_24T_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")

#DOX24R
venn_DOX_24R_RUV <- getSet(object = venn_test_RUV, subset = c("Group 2"))
dim(venn_DOX_24R_RUV)

[1] 2107    2

#2107 genes in DOX_24R only

venn_DOX24R_DEGs_RUV <- venn_DOX_24R_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_24R_DEGs_RUV <- Toptable_list_RUVk1_symbols$V.D24R_RUV[row.names(venn_DOX24R_DEGs_RUV),]

DOX24R_DEGs_GO_RUV <- DOX_24R_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")


#DOX144R
venn_DOX_144R_RUV <- getSet(object = venn_test_RUV, subset = c("Group 3"))
dim(venn_DOX_144R_RUV)

[1] 52  2

#52 genes in DOX_144R only

venn_DOX144R_DEGs_RUV <- venn_DOX_144R_RUV %>% 
  as.data.frame() %>% 
  column_to_rownames(., var = "Detail")

#pull these genes out of my DEG matrix with logFC
DOX_144R_DEGs_RUV <- 
  Toptable_list_RUVk1_symbols$V.D144R_RUV[row.names(venn_DOX144R_DEGs_RUV),]

DOX144R_DEGs_GO_RUV <- DOX_144R_DEGs_RUV %>% 
  dplyr::filter(., adj.P.Val < 0.05) %>% 
  dplyr::select("Entrez_ID")

###GO KEGG Overlap of DEGs From Original Data

#####DOX24 Genes#####
library(gprofiler2)

D24_DEGs_mat <- as.matrix(DOX24T_DEGs_GO)

DOX_24_dxr_gene <- gost(query = D24_DEGs_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24_gost_genes <- gostplot(DOX_24_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24_gost_genes

table_DOX24_genes <- DOX_24_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	1355	5390	2.955e-59
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	1046	3990	3.142e-51
GO:BP	GO:0051252	regulation of RNA metabolic process	965	3687	5.969e-46
GO:BP	GO:0006351	DNA-templated transcription	930	3549	3.382e-44
GO:BP	GO:0019538	protein metabolic process	1153	4721	5.625e-41
GO:BP	GO:2001141	regulation of RNA biosynthetic process	890	3428	3.256e-40
GO:BP	GO:0006355	regulation of DNA-templated transcription	886	3409	3.256e-40
GO:BP	GO:0043412	macromolecule modification	773	3030	5.277e-31
GO:BP	GO:0006996	organelle organization	885	3594	1.783e-30
GO:BP	GO:0006366	transcription by RNA polymerase II	704	2711	2.695e-30
GO:BP	GO:0019222	regulation of metabolic process	1539	7035	9.797e-30
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	667	2578	5.907e-28
GO:BP	GO:0044238	primary metabolic process	2457	12342	2.653e-27
GO:BP	GO:0060255	regulation of macromolecule metabolic process	1422	6492	1.244e-26
GO:BP	GO:0048522	positive regulation of cellular process	1310	5920	1.249e-25
GO:BP	GO:0036211	protein modification process	708	2846	1.236e-24
GO:BP	GO:0048518	positive regulation of biological process	1368	6264	1.493e-24
GO:BP	GO:0009056	catabolic process	659	2639	4.202e-23
GO:BP	GO:0046907	intracellular transport	392	1381	6.275e-23
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	531	2036	2.149e-22
GO:BP	GO:0009893	positive regulation of metabolic process	846	3597	4.099e-22
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	782	3288	1.586e-21
GO:BP	GO:0050789	regulation of biological process	2420	12336	3.330e-21
GO:BP	GO:0050794	regulation of cellular process	2352	11946	6.778e-21
GO:BP	GO:0065007	biological regulation	2484	12743	1.666e-20
GO:BP	GO:0009889	regulation of biosynthetic process	1255	5809	8.803e-20
GO:BP	GO:0006412	translation	232	727	1.113e-19
GO:BP	GO:0051254	positive regulation of RNA metabolic process	477	1835	1.337e-19
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1219	5644	5.900e-19
GO:BP	GO:0051649	establishment of localization in cell	509	2010	1.547e-18
GO:BP	GO:0033554	cellular response to stress	471	1830	1.968e-18
GO:BP	GO:0009057	macromolecule catabolic process	383	1417	2.239e-18
GO:BP	GO:0010468	regulation of gene expression	1192	5536	6.806e-18
GO:BP	GO:0033036	macromolecule localization	748	3228	2.540e-17
GO:BP	GO:0051641	cellular localization	832	3661	3.002e-17
GO:BP	GO:0140053	mitochondrial gene expression	80	168	4.505e-17
GO:BP	GO:0006325	chromatin organization	260	884	6.229e-17
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	436	1697	8.309e-17
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	436	1699	1.019e-16
GO:BP	GO:0043687	post-translational protein modification	290	1027	2.501e-16
GO:BP	GO:0015031	protein transport	377	1444	1.835e-15
GO:BP	GO:0032446	protein modification by small protein conjugation	248	853	1.909e-15
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	274	975	4.505e-15
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	610	2593	4.718e-15
GO:BP	GO:0009891	positive regulation of biosynthetic process	629	2696	8.660e-15
GO:BP	GO:0008104	protein localization	643	2770	1.110e-14
GO:BP	GO:0070727	cellular macromolecule localization	645	2782	1.270e-14
GO:BP	GO:0008152	metabolic process	2676	14136	1.403e-14
GO:BP	GO:0071705	nitrogen compound transport	470	1923	4.476e-14
GO:BP	GO:0051128	regulation of cellular component organization	570	2433	1.473e-13
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	386	1529	1.765e-13
GO:BP	GO:0030163	protein catabolic process	280	1030	1.765e-13
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	226	786	1.827e-13
GO:BP	GO:0006886	intracellular protein transport	203	686	2.250e-13
GO:BP	GO:0009894	regulation of catabolic process	281	1040	3.402e-13
GO:BP	GO:0006259	DNA metabolic process	273	1005	4.258e-13
GO:BP	GO:0042254	ribosome biogenesis	115	323	4.644e-13
GO:BP	GO:0035556	intracellular signal transduction	670	2965	8.507e-13
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	191	643	9.822e-13
GO:BP	GO:0016567	protein ubiquitination	218	768	2.362e-12
GO:BP	GO:0019941	modification-dependent protein catabolic process	188	638	3.636e-12
GO:BP	GO:0006974	DNA damage response	248	908	4.093e-12
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	184	628	1.200e-11
GO:BP	GO:0032543	mitochondrial translation	59	130	2.039e-11
GO:BP	GO:0051253	negative regulation of RNA metabolic process	349	1400	2.520e-11
GO:BP	GO:0006281	DNA repair	181	621	3.090e-11
GO:BP	GO:0006338	chromatin remodeling	204	725	3.859e-11
GO:BP	GO:0023051	regulation of signaling	758	3478	3.859e-11
GO:BP	GO:1903311	regulation of mRNA metabolic process	107	312	5.829e-11
GO:BP	GO:0048583	regulation of response to stimulus	854	3993	6.640e-11
GO:BP	GO:0051179	localization	1144	5555	8.041e-11
GO:BP	GO:0010646	regulation of cell communication	757	3486	8.628e-11
GO:BP	GO:0048523	negative regulation of cellular process	1157	5629	9.293e-11
GO:BP	GO:0009966	regulation of signal transduction	670	3034	9.639e-11
GO:BP	GO:0010498	proteasomal protein catabolic process	161	543	1.299e-10
GO:BP	GO:0006402	mRNA catabolic process	93	261	1.507e-10
GO:BP	GO:0009987	cellular process	3598	20247	1.644e-10
GO:BP	GO:0033043	regulation of organelle organization	292	1148	2.045e-10
GO:BP	GO:0045184	establishment of protein localization	453	1937	2.074e-10
GO:BP	GO:0051246	regulation of protein metabolic process	436	1855	2.638e-10
GO:BP	GO:0006403	RNA localization	76	200	4.297e-10
GO:BP	GO:0051169	nuclear transport	109	334	1.044e-09
GO:BP	GO:0006913	nucleocytoplasmic transport	109	334	1.044e-09
GO:BP	GO:0007005	mitochondrion organization	133	435	1.075e-09
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	156	535	1.096e-09
GO:BP	GO:0006796	phosphate-containing compound metabolic process	540	2407	1.767e-09
GO:BP	GO:0060341	regulation of cellular localization	259	1013	2.043e-09
GO:BP	GO:0006793	phosphorus metabolic process	540	2410	2.139e-09
GO:BP	GO:0051052	regulation of DNA metabolic process	147	500	2.152e-09
GO:BP	GO:0080135	regulation of cellular response to stress	151	519	2.682e-09
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	308	1256	4.235e-09
GO:BP	GO:0043484	regulation of RNA splicing	70	187	5.937e-09
GO:BP	GO:0006399	tRNA metabolic process	76	210	5.957e-09
GO:BP	GO:0016072	rRNA metabolic process	90	266	7.047e-09
GO:BP	GO:0006810	transport	915	4407	7.401e-09
GO:BP	GO:0071840	cellular component organization or biogenesis	1637	8393	8.414e-09
GO:BP	GO:0048519	negative regulation of biological process	1177	5834	8.512e-09
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	125	414	9.665e-09
GO:BP	GO:0009896	positive regulation of catabolic process	155	546	1.007e-08
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	314	1296	1.067e-08
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	310	1280	1.473e-08
GO:BP	GO:0007049	cell cycle	387	1663	1.672e-08
GO:BP	GO:0051168	nuclear export	64	169	1.969e-08
GO:BP	GO:0032880	regulation of protein localization	232	907	1.969e-08
GO:BP	GO:0061919	process utilizing autophagic mechanism	165	597	2.219e-08
GO:BP	GO:0006914	autophagy	165	597	2.219e-08
GO:BP	GO:0009968	negative regulation of signal transduction	318	1326	2.573e-08
GO:BP	GO:0051726	regulation of cell cycle	268	1087	4.096e-08
GO:BP	GO:0038202	TORC1 signaling	45	103	4.353e-08
GO:BP	GO:0000209	protein polyubiquitination	91	280	5.172e-08
GO:BP	GO:0006302	double-strand break repair	99	319	1.523e-07
GO:BP	GO:0006401	RNA catabolic process	98	315	1.576e-07
GO:BP	GO:0006364	rRNA processing	76	225	1.901e-07
GO:BP	GO:0023057	negative regulation of signaling	335	1435	1.999e-07
GO:BP	GO:0051236	establishment of RNA localization	60	163	2.334e-07
GO:BP	GO:0010648	negative regulation of cell communication	334	1436	3.186e-07
GO:BP	GO:0006417	regulation of translation	112	380	3.464e-07
GO:BP	GO:0032259	methylation	78	236	3.464e-07
GO:BP	GO:0006282	regulation of DNA repair	75	225	4.441e-07
GO:BP	GO:0008033	tRNA processing	53	139	4.518e-07
GO:BP	GO:0061013	regulation of mRNA catabolic process	68	198	5.697e-07
GO:BP	GO:0031929	TOR signaling	60	167	6.369e-07
GO:BP	GO:1904262	negative regulation of TORC1 signaling	26	48	7.306e-07
GO:BP	GO:0050658	RNA transport	58	160	7.544e-07
GO:BP	GO:0050657	nucleic acid transport	58	160	7.544e-07
GO:BP	GO:0051234	establishment of localization	992	4928	8.478e-07
GO:BP	GO:0043170	macromolecule metabolic process	2253	12048	8.593e-07
GO:BP	GO:0009895	negative regulation of catabolic process	106	361	1.031e-06
GO:BP	GO:0043488	regulation of mRNA stability	63	181	1.056e-06
GO:BP	GO:1903432	regulation of TORC1 signaling	40	96	1.713e-06
GO:BP	GO:0141188	nucleic acid catabolic process	101	343	1.879e-06
GO:BP	GO:0018193	peptidyl-amino acid modification	176	686	1.982e-06
GO:BP	GO:0048585	negative regulation of response to stimulus	377	1680	2.059e-06
GO:BP	GO:1902531	regulation of intracellular signal transduction	430	1953	2.226e-06
GO:BP	GO:0033044	regulation of chromosome organization	77	242	2.424e-06
GO:BP	GO:0043487	regulation of RNA stability	65	193	2.549e-06
GO:BP	GO:0043414	macromolecule methylation	48	127	2.832e-06
GO:BP	GO:0006139	nucleobase-containing compound metabolic process	1536	7992	4.411e-06
GO:BP	GO:0015931	nucleobase-containing compound transport	75	237	4.544e-06
GO:BP	GO:0016073	snRNA metabolic process	28	58	4.722e-06
GO:BP	GO:0000278	mitotic cell cycle	217	892	4.767e-06
GO:BP	GO:0032007	negative regulation of TOR signaling	31	68	4.989e-06
GO:BP	GO:0061024	membrane organization	202	821	5.548e-06
GO:BP	GO:0051028	mRNA transport	48	130	6.186e-06
GO:BP	GO:0019637	organophosphate metabolic process	254	1077	6.186e-06
GO:BP	GO:0080134	regulation of response to stress	316	1387	6.186e-06
GO:BP	GO:0048193	Golgi vesicle transport	92	312	6.454e-06
GO:BP	GO:0006839	mitochondrial transport	60	178	7.486e-06
GO:BP	GO:0009451	RNA modification	59	174	7.486e-06
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	47	127	7.535e-06
GO:BP	GO:0032204	regulation of telomere maintenance	43	112	7.667e-06
GO:BP	GO:0032879	regulation of localization	440	2029	8.883e-06
GO:BP	GO:0007275	multicellular organism development	944	4727	9.559e-06
GO:BP	GO:0065009	regulation of molecular function	336	1496	9.987e-06
GO:BP	GO:0032790	ribosome disassembly	22	41	1.013e-05
GO:BP	GO:0016043	cellular component organization	1565	8184	1.067e-05
GO:BP	GO:0098727	maintenance of cell number	61	184	1.087e-05
GO:BP	GO:0022402	cell cycle process	293	1280	1.097e-05
GO:BP	GO:0070925	organelle assembly	246	1046	1.164e-05
GO:BP	GO:0000725	recombinational repair	63	193	1.269e-05
GO:BP	GO:1903047	mitotic cell cycle process	184	745	1.424e-05
GO:BP	GO:0048584	positive regulation of response to stimulus	496	2331	1.443e-05
GO:BP	GO:0051276	chromosome organization	148	574	1.495e-05
GO:BP	GO:0051130	positive regulation of cellular component organization	257	1105	1.601e-05
GO:BP	GO:0010638	positive regulation of organelle organization	130	492	1.894e-05
GO:BP	GO:0006383	transcription by RNA polymerase III	28	62	2.318e-05
GO:BP	GO:0000724	double-strand break repair via homologous recombination	61	188	2.369e-05
GO:BP	GO:0051716	cellular response to stimulus	1417	7376	2.369e-05
GO:BP	GO:0019827	stem cell population maintenance	59	180	2.468e-05
GO:BP	GO:0070585	protein localization to mitochondrion	47	132	2.503e-05
GO:BP	GO:0000723	telomere maintenance	55	164	2.600e-05
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	222	938	2.638e-05
GO:BP	GO:0034504	protein localization to nucleus	91	318	2.819e-05
GO:BP	GO:0006457	protein folding	68	219	3.219e-05
GO:BP	GO:0009892	negative regulation of metabolic process	688	3375	4.056e-05
GO:BP	GO:0032006	regulation of TOR signaling	50	146	4.083e-05
GO:BP	GO:0051247	positive regulation of protein metabolic process	241	1039	4.414e-05
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	44	123	4.752e-05
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	164	662	4.752e-05
GO:BP	GO:1903008	organelle disassembly	30	71	4.845e-05
GO:BP	GO:0006950	response to stress	793	3948	4.923e-05
GO:BP	GO:0008219	cell death	426	1991	5.646e-05
GO:BP	GO:0007006	mitochondrial membrane organization	42	116	5.648e-05
GO:BP	GO:1901135	carbohydrate derivative metabolic process	229	983	5.742e-05
GO:BP	GO:0012501	programmed cell death	425	1987	5.949e-05
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	49	144	6.152e-05
GO:BP	GO:0017004	cytochrome complex assembly	21	42	7.496e-05
GO:BP	GO:0032502	developmental process	1263	6553	7.983e-05
GO:BP	GO:0051604	protein maturation	137	539	8.325e-05
GO:BP	GO:0007346	regulation of mitotic cell cycle	127	492	8.464e-05
GO:BP	GO:0006405	RNA export from nucleus	35	91	8.464e-05
GO:BP	GO:0006508	proteolysis	327	1486	8.760e-05
GO:BP	GO:0044281	small molecule metabolic process	383	1776	8.962e-05
GO:BP	GO:0006400	tRNA modification	36	95	8.988e-05
GO:BP	GO:0051054	positive regulation of DNA metabolic process	83	291	9.029e-05
GO:BP	GO:0048856	anatomical structure development	1162	5997	9.554e-05
GO:BP	GO:0006390	mitochondrial transcription	14	22	9.554e-05
GO:BP	GO:0016192	vesicle-mediated transport	347	1592	1.019e-04
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	39	107	1.025e-04
GO:BP	GO:0050793	regulation of developmental process	512	2457	1.025e-04
GO:BP	GO:0010564	regulation of cell cycle process	174	720	1.049e-04
GO:BP	GO:0033365	protein localization to organelle	272	1209	1.082e-04
GO:BP	GO:0051248	negative regulation of protein metabolic process	165	677	1.116e-04
GO:BP	GO:2000779	regulation of double-strand break repair	48	143	1.116e-04
GO:BP	GO:0031123	RNA 3’-end processing	36	96	1.134e-04
GO:BP	GO:0006487	protein N-linked glycosylation	30	74	1.202e-04
GO:BP	GO:0007004	telomere maintenance via telomerase	26	60	1.262e-04
GO:BP	GO:0072344	rescue of stalled ribosome	18	34	1.327e-04
GO:BP	GO:0018205	peptidyl-lysine modification	47	140	1.376e-04
GO:BP	GO:0010506	regulation of autophagy	99	367	1.409e-04
GO:BP	GO:0006753	nucleoside phosphate metabolic process	158	646	1.411e-04
GO:BP	GO:0023056	positive regulation of signaling	385	1796	1.411e-04
GO:BP	GO:0022411	cellular component disassembly	116	446	1.429e-04
GO:BP	GO:0043009	chordate embryonic development	163	671	1.496e-04
GO:BP	GO:0006915	apoptotic process	409	1923	1.517e-04
GO:BP	GO:0030522	intracellular receptor signaling pathway	101	377	1.520e-04
GO:BP	GO:1903829	positive regulation of protein localization	127	499	1.607e-04
GO:BP	GO:0009790	embryo development	256	1135	1.648e-04
GO:BP	GO:0016055	Wnt signaling pathway	118	458	1.868e-04
GO:BP	GO:0009967	positive regulation of signal transduction	342	1578	1.868e-04
GO:BP	GO:0043067	regulation of programmed cell death	328	1506	1.907e-04
GO:BP	GO:0030030	cell projection organization	352	1631	1.978e-04
GO:BP	GO:0006354	DNA-templated transcription elongation	45	134	2.050e-04
GO:BP	GO:0050684	regulation of mRNA processing	45	134	2.050e-04
GO:BP	GO:0006458	‘de novo’ protein folding	22	48	2.220e-04
GO:BP	GO:0010647	positive regulation of cell communication	383	1795	2.237e-04
GO:BP	GO:0006414	translational elongation	31	80	2.301e-04
GO:BP	GO:0031647	regulation of protein stability	91	335	2.362e-04
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	29	73	2.560e-04
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	162	673	2.603e-04
GO:BP	GO:0000959	mitochondrial RNA metabolic process	23	52	2.788e-04
GO:BP	GO:0006626	protein targeting to mitochondrion	37	104	3.066e-04
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	26	63	3.334e-04
GO:BP	GO:0044093	positive regulation of molecular function	204	884	3.373e-04
GO:BP	GO:0032386	regulation of intracellular transport	75	266	3.632e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	165	692	3.711e-04
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	21	46	3.727e-04
GO:BP	GO:0016236	macroautophagy	96	362	3.769e-04
GO:BP	GO:0042981	regulation of apoptotic process	317	1462	3.805e-04
GO:BP	GO:0051170	import into nucleus	53	171	4.185e-04
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	68	236	4.185e-04
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	20	43	4.210e-04
GO:BP	GO:0016310	phosphorylation	289	1320	4.358e-04
GO:BP	GO:0170036	import into the mitochondrion	22	50	4.628e-04
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	88	327	4.628e-04
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	36	102	4.677e-04
GO:BP	GO:0061157	mRNA destabilization	36	102	4.677e-04
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	41	122	4.708e-04
GO:BP	GO:0050779	RNA destabilization	37	106	4.708e-04
GO:BP	GO:0042176	regulation of protein catabolic process	97	369	4.777e-04
GO:BP	GO:0051129	negative regulation of cellular component organization	166	701	4.950e-04
GO:BP	GO:0006289	nucleotide-excision repair	31	83	5.001e-04
GO:BP	GO:0009267	cellular response to starvation	54	177	5.466e-04
GO:BP	GO:0141124	intracellular signaling cassette	401	1912	6.502e-04
GO:BP	GO:0032200	telomere organization	57	191	6.559e-04
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	34	96	7.188e-04
GO:BP	GO:0042274	ribosomal small subunit biogenesis	36	104	7.345e-04
GO:BP	GO:0006606	protein import into nucleus	51	166	7.425e-04
GO:BP	GO:0010256	endomembrane system organization	147	613	7.575e-04
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	23	55	7.649e-04
GO:BP	GO:1990253	cellular response to leucine starvation	9	12	7.656e-04
GO:BP	GO:0045739	positive regulation of DNA repair	44	137	7.973e-04
GO:BP	GO:0090304	nucleic acid metabolic process	1405	7434	8.003e-04
GO:BP	GO:0007399	nervous system development	530	2604	8.126e-04
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	47	150	8.620e-04
GO:BP	GO:0046434	organophosphate catabolic process	69	246	8.692e-04
GO:BP	GO:0010507	negative regulation of autophagy	33	93	8.699e-04
GO:BP	GO:0070201	regulation of establishment of protein localization	131	537	8.708e-04
GO:BP	GO:0007007	inner mitochondrial membrane organization	20	45	8.749e-04
GO:BP	GO:0050821	protein stabilization	64	224	8.960e-04
GO:BP	GO:0019693	ribose phosphate metabolic process	98	380	9.194e-04
GO:BP	GO:0044087	regulation of cellular component biogenesis	226	1011	9.206e-04
GO:BP	GO:0072521	purine-containing compound metabolic process	136	563	1.001e-03
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	14	26	1.026e-03
GO:BP	GO:0009259	ribonucleotide metabolic process	96	372	1.061e-03
GO:BP	GO:0031669	cellular response to nutrient levels	69	248	1.114e-03
GO:BP	GO:2000780	negative regulation of double-strand break repair	18	39	1.160e-03
GO:BP	GO:0032206	positive regulation of telomere maintenance	28	75	1.186e-03
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	94	364	1.224e-03
GO:BP	GO:0002181	cytoplasmic translation	50	165	1.232e-03
GO:BP	GO:0016197	endosomal transport	78	290	1.263e-03
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	30	83	1.276e-03
GO:BP	GO:0009150	purine ribonucleotide metabolic process	91	351	1.364e-03
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	51	170	1.371e-03
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	43	136	1.379e-03
GO:BP	GO:1901987	regulation of cell cycle phase transition	107	427	1.395e-03
GO:BP	GO:0007030	Golgi organization	47	153	1.395e-03
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	336	1588	1.420e-03
GO:BP	GO:0006310	DNA recombination	90	347	1.445e-03
GO:BP	GO:0010639	negative regulation of organelle organization	91	352	1.492e-03
GO:BP	GO:2000278	regulation of DNA biosynthetic process	32	92	1.659e-03
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	13	24	1.725e-03
GO:BP	GO:0071495	cellular response to endogenous stimulus	265	1223	1.812e-03
GO:BP	GO:1901292	nucleoside phosphate catabolic process	54	185	1.830e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	546	2713	1.882e-03
GO:BP	GO:0009117	nucleotide metabolic process	120	493	1.884e-03
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	628	3157	1.884e-03
GO:BP	GO:0030111	regulation of Wnt signaling pathway	86	331	1.919e-03
GO:BP	GO:0072523	purine-containing compound catabolic process	47	155	1.919e-03
GO:BP	GO:0045727	positive regulation of translation	43	138	1.926e-03
GO:BP	GO:0001510	RNA methylation	29	81	1.961e-03
GO:BP	GO:0007017	microtubule-based process	221	999	2.012e-03
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	69	253	2.012e-03
GO:BP	GO:0043543	protein acylation	31	89	2.012e-03
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	59	208	2.026e-03
GO:BP	GO:0006997	nucleus organization	45	147	2.074e-03
GO:BP	GO:0007059	chromosome segregation	106	427	2.115e-03
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	16	34	2.136e-03
GO:BP	GO:0001701	in utero embryonic development	103	413	2.182e-03
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	38	118	2.243e-03
GO:BP	GO:0045738	negative regulation of DNA repair	18	41	2.350e-03
GO:BP	GO:0031399	regulation of protein modification process	230	1049	2.496e-03
GO:BP	GO:0006413	translational initiation	40	127	2.530e-03
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	44	144	2.544e-03
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	24	63	2.583e-03
GO:BP	GO:0042594	response to starvation	61	219	2.632e-03
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	70	260	2.646e-03
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	70	260	2.646e-03
GO:BP	GO:0090685	RNA localization to nucleus	11	19	2.681e-03
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	88	344	2.681e-03
GO:BP	GO:0090670	RNA localization to Cajal body	11	19	2.681e-03
GO:BP	GO:0090671	telomerase RNA localization to Cajal body	11	19	2.681e-03
GO:BP	GO:0090672	telomerase RNA localization	11	19	2.681e-03
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	11	19	2.681e-03
GO:BP	GO:0009261	ribonucleotide catabolic process	42	136	2.699e-03
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	56	197	2.699e-03
GO:BP	GO:0018279	protein N-linked glycosylation via asparagine	19	45	2.709e-03
GO:BP	GO:0017148	negative regulation of translation	41	132	2.804e-03
GO:BP	GO:1902903	regulation of supramolecular fiber organization	96	383	2.919e-03
GO:BP	GO:0048731	system development	789	4053	2.940e-03
GO:BP	GO:0010948	negative regulation of cell cycle process	76	289	2.986e-03
GO:BP	GO:0040029	epigenetic regulation of gene expression	78	299	3.225e-03
GO:BP	GO:0007033	vacuole organization	65	239	3.225e-03
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	37	116	3.225e-03
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	70	262	3.242e-03
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	73	276	3.282e-03
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	139	594	3.282e-03
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	36	112	3.294e-03
GO:BP	GO:0044772	mitotic cell cycle phase transition	105	428	3.389e-03
GO:BP	GO:0034198	cellular response to amino acid starvation	21	53	3.411e-03
GO:BP	GO:0051640	organelle localization	144	620	3.565e-03
GO:BP	GO:0051865	protein autoubiquitination	27	76	3.565e-03
GO:BP	GO:0042149	cellular response to glucose starvation	19	46	3.664e-03
GO:BP	GO:0031124	mRNA 3’-end processing	19	46	3.664e-03
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	38	121	3.664e-03
GO:BP	GO:1904874	positive regulation of telomerase RNA localization to Cajal body	7	9	3.723e-03
GO:BP	GO:0042796	snRNA transcription by RNA polymerase III	7	9	3.723e-03
GO:BP	GO:0006163	purine nucleotide metabolic process	105	430	3.997e-03
GO:BP	GO:0035967	cellular response to topologically incorrect protein	35	109	4.037e-03
GO:BP	GO:0051091	positive regulation of DNA-binding transcription factor activity	55	196	4.195e-03
GO:BP	GO:0048255	mRNA stabilization	25	69	4.276e-03
GO:BP	GO:0051053	negative regulation of DNA metabolic process	42	139	4.296e-03
GO:BP	GO:0006468	protein phosphorylation	262	1227	4.554e-03
GO:BP	GO:0009301	snRNA transcription	11	20	4.580e-03
GO:BP	GO:0030150	protein import into mitochondrial matrix	11	20	4.580e-03
GO:BP	GO:0031503	protein-containing complex localization	59	215	4.716e-03
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	82	322	4.834e-03
GO:BP	GO:0000226	microtubule cytoskeleton organization	153	670	4.970e-03
GO:BP	GO:0051049	regulation of transport	334	1607	4.970e-03
GO:BP	GO:0009166	nucleotide catabolic process	47	162	5.163e-03
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	32	98	5.212e-03
GO:BP	GO:0007010	cytoskeleton organization	319	1529	5.212e-03
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	61	225	5.212e-03
GO:BP	GO:0072175	epithelial tube formation	41	136	5.226e-03
GO:BP	GO:0006406	mRNA export from nucleus	25	70	5.333e-03
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	25	70	5.333e-03
GO:BP	GO:0061077	chaperone-mediated protein folding	26	74	5.416e-03
GO:BP	GO:0044770	cell cycle phase transition	125	532	5.449e-03
GO:BP	GO:0008535	respiratory chain complex IV assembly	14	30	5.706e-03
GO:BP	GO:1904872	regulation of telomerase RNA localization to Cajal body	8	12	5.887e-03
GO:BP	GO:1904867	protein localization to Cajal body	8	12	5.887e-03
GO:BP	GO:1905456	regulation of lymphoid progenitor cell differentiation	8	12	5.887e-03
GO:BP	GO:1904951	positive regulation of establishment of protein localization	83	329	5.887e-03
GO:BP	GO:1903405	protein localization to nuclear body	8	12	5.887e-03
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	49	172	5.911e-03
GO:BP	GO:0071897	DNA biosynthetic process	49	172	5.911e-03
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	70	268	5.999e-03
GO:BP	GO:0070936	protein K48-linked ubiquitination	32	99	6.167e-03
GO:BP	GO:0048468	cell development	569	2876	6.246e-03
GO:BP	GO:0033119	negative regulation of RNA splicing	13	27	6.295e-03
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	13	27	6.295e-03
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	40	133	6.295e-03
GO:BP	GO:0060070	canonical Wnt signaling pathway	79	311	6.382e-03
GO:BP	GO:0008213	protein alkylation	19	48	6.386e-03
GO:BP	GO:0006479	protein methylation	19	48	6.386e-03
GO:BP	GO:1902369	negative regulation of RNA catabolic process	30	91	6.386e-03
GO:BP	GO:0048285	organelle fission	118	500	6.407e-03
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	42	142	6.507e-03
GO:BP	GO:0009154	purine ribonucleotide catabolic process	39	129	6.507e-03
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	27	79	6.511e-03
GO:BP	GO:0071559	response to transforming growth factor beta	70	269	6.511e-03
GO:BP	GO:0031109	microtubule polymerization or depolymerization	41	138	6.814e-03
GO:BP	GO:0006195	purine nucleotide catabolic process	41	138	6.814e-03
GO:BP	GO:0051223	regulation of protein transport	106	442	6.814e-03
GO:BP	GO:0062125	regulation of mitochondrial gene expression	15	34	6.869e-03
GO:BP	GO:0021915	neural tube development	46	160	6.869e-03
GO:BP	GO:0030258	lipid modification	54	196	7.010e-03
GO:BP	GO:0010970	transport along microtubule	50	178	7.010e-03
GO:BP	GO:0062197	cellular response to chemical stress	80	317	7.010e-03
GO:BP	GO:1990928	response to amino acid starvation	21	56	7.204e-03
GO:BP	GO:0090110	COPII-coated vesicle cargo loading	10	18	7.306e-03
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	38	126	7.909e-03
GO:BP	GO:2000036	regulation of stem cell population maintenance	25	72	7.948e-03
GO:BP	GO:0016226	iron-sulfur cluster assembly	14	31	7.948e-03
GO:BP	GO:0031163	metallo-sulfur cluster assembly	14	31	7.948e-03
GO:BP	GO:0019080	viral gene expression	34	109	7.948e-03
GO:BP	GO:0000966	RNA 5’-end processing	16	38	8.082e-03
GO:BP	GO:0035148	tube formation	43	148	8.091e-03
GO:BP	GO:0000819	sister chromatid segregation	62	234	8.121e-03
GO:BP	GO:2001252	positive regulation of chromosome organization	33	105	8.203e-03
GO:BP	GO:0140694	membraneless organelle assembly	103	430	8.270e-03
GO:BP	GO:0000070	mitotic sister chromatid segregation	53	193	8.347e-03
GO:BP	GO:0000045	autophagosome assembly	36	118	8.553e-03
GO:BP	GO:0018216	peptidyl-arginine methylation	7	10	8.784e-03
GO:BP	GO:1904871	positive regulation of protein localization to Cajal body	7	10	8.784e-03
GO:BP	GO:1904869	regulation of protein localization to Cajal body	7	10	8.784e-03
GO:BP	GO:0001837	epithelial to mesenchymal transition	48	171	8.905e-03
GO:BP	GO:0044782	cilium organization	103	431	8.905e-03
GO:BP	GO:0140014	mitotic nuclear division	72	282	9.147e-03
GO:BP	GO:0061053	somite development	28	85	9.407e-03
GO:BP	GO:0000460	maturation of 5.8S rRNA	15	35	9.450e-03
GO:BP	GO:0016180	snRNA processing	15	35	9.450e-03
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	15	35	9.450e-03
GO:BP	GO:0009058	biosynthetic process	1952	10664	9.681e-03
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	42	145	9.715e-03
GO:BP	GO:0045017	glycerolipid biosynthetic process	65	250	9.968e-03
GO:BP	GO:0050790	regulation of catalytic activity	201	928	1.004e-02
GO:BP	GO:0051098	regulation of binding	57	213	1.008e-02
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	66	255	1.027e-02
GO:BP	GO:1990542	mitochondrial transmembrane transport	31	98	1.030e-02
GO:BP	GO:0000902	cell morphogenesis	214	996	1.037e-02
GO:BP	GO:0009890	negative regulation of biosynthetic process	554	2813	1.049e-02
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	49	177	1.062e-02
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	49	177	1.062e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	555	2819	1.062e-02
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	16	39	1.071e-02
GO:BP	GO:0090181	regulation of cholesterol metabolic process	16	39	1.071e-02
GO:BP	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	14	32	1.101e-02
GO:BP	GO:0001682	tRNA 5’-leader removal	8	13	1.104e-02
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	33	107	1.115e-02
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	44	155	1.115e-02
GO:BP	GO:0046890	regulation of lipid biosynthetic process	50	182	1.115e-02
GO:BP	GO:0002833	positive regulation of response to biotic stimulus	96	400	1.117e-02
GO:BP	GO:0042770	signal transduction in response to DNA damage	48	173	1.118e-02
GO:BP	GO:0016050	vesicle organization	91	376	1.147e-02
GO:BP	GO:0043489	RNA stabilization	26	78	1.147e-02
GO:BP	GO:0034599	cellular response to oxidative stress	64	247	1.153e-02
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	32	103	1.153e-02
GO:BP	GO:0099116	tRNA 5’-end processing	9	16	1.178e-02
GO:BP	GO:0006650	glycerophospholipid metabolic process	77	309	1.200e-02
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	40	138	1.222e-02
GO:BP	GO:0032984	protein-containing complex disassembly	66	257	1.225e-02
GO:BP	GO:0007264	small GTPase-mediated signal transduction	117	505	1.229e-02
GO:BP	GO:0043254	regulation of protein-containing complex assembly	100	421	1.232e-02
GO:BP	GO:0022008	neurogenesis	360	1771	1.232e-02
GO:BP	GO:0045786	negative regulation of cell cycle	91	377	1.232e-02
GO:BP	GO:1905037	autophagosome organization	37	125	1.235e-02
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	18	47	1.251e-02
GO:BP	GO:1902745	positive regulation of lamellipodium organization	15	36	1.254e-02
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	64	248	1.258e-02
GO:BP	GO:2000973	regulation of pro-B cell differentiation	6	8	1.258e-02
GO:BP	GO:0051086	chaperone mediated protein folding independent of cofactor	6	8	1.258e-02
GO:BP	GO:1902115	regulation of organelle assembly	61	234	1.259e-02
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	79	320	1.340e-02
GO:BP	GO:0031400	negative regulation of protein modification process	85	349	1.342e-02
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	38	130	1.344e-02
GO:BP	GO:0140374	antiviral innate immune response	20	55	1.360e-02
GO:BP	GO:0008610	lipid biosynthetic process	161	729	1.361e-02
GO:BP	GO:0051493	regulation of cytoskeleton organization	119	517	1.387e-02
GO:BP	GO:0006998	nuclear envelope organization	21	59	1.387e-02
GO:BP	GO:0009303	rRNA transcription	16	40	1.391e-02
GO:BP	GO:0035966	response to topologically incorrect protein	44	157	1.403e-02
GO:BP	GO:0045089	positive regulation of innate immune response	90	374	1.407e-02
GO:BP	GO:0033617	mitochondrial cytochrome c oxidase assembly	12	26	1.427e-02
GO:BP	GO:2000737	negative regulation of stem cell differentiation	12	26	1.427e-02
GO:BP	GO:0044092	negative regulation of molecular function	126	553	1.468e-02
GO:BP	GO:0031116	positive regulation of microtubule polymerization	14	33	1.473e-02
GO:BP	GO:0070085	glycosylation	63	245	1.473e-02
GO:BP	GO:0045995	regulation of embryonic development	29	92	1.486e-02
GO:BP	GO:0060562	epithelial tube morphogenesis	82	336	1.497e-02
GO:BP	GO:0009719	response to endogenous stimulus	306	1489	1.497e-02
GO:BP	GO:0090407	organophosphate biosynthetic process	139	619	1.497e-02
GO:BP	GO:0000075	cell cycle checkpoint signaling	50	185	1.529e-02
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	32	105	1.544e-02
GO:BP	GO:0034314	Arp2/3 complex-mediated actin nucleation	18	48	1.582e-02
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	56	213	1.582e-02
GO:BP	GO:1900151	regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	11	23	1.609e-02
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	39	136	1.653e-02
GO:BP	GO:0034976	response to endoplasmic reticulum stress	68	270	1.667e-02
GO:BP	GO:0045732	positive regulation of protein catabolic process	55	209	1.696e-02
GO:BP	GO:0001838	embryonic epithelial tube formation	36	123	1.704e-02
GO:BP	GO:0062028	regulation of stress granule assembly	7	11	1.726e-02
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	75	304	1.726e-02
GO:BP	GO:0018195	peptidyl-arginine modification	7	11	1.726e-02
GO:BP	GO:1904357	negative regulation of telomere maintenance via telomere lengthening	13	30	1.726e-02
GO:BP	GO:0046834	lipid phosphorylation	7	11	1.726e-02
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	75	304	1.726e-02
GO:BP	GO:0019220	regulation of phosphate metabolic process	204	956	1.732e-02
GO:BP	GO:2000781	positive regulation of double-strand break repair	29	93	1.732e-02
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	538	2745	1.732e-02
GO:BP	GO:0016482	cytosolic transport	40	141	1.749e-02
GO:BP	GO:0010212	response to ionizing radiation	40	141	1.749e-02
GO:BP	GO:0048762	mesenchymal cell differentiation	64	252	1.803e-02
GO:BP	GO:1901701	cellular response to oxygen-containing compound	247	1182	1.804e-02
GO:BP	GO:0051174	regulation of phosphorus metabolic process	204	957	1.811e-02
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	45	164	1.862e-02
GO:BP	GO:1990173	protein localization to nucleoplasm	8	14	1.882e-02
GO:BP	GO:0098734	macromolecule depalmitoylation	8	14	1.882e-02
GO:BP	GO:0043144	sno(s)RNA processing	8	14	1.882e-02
GO:BP	GO:0019216	regulation of lipid metabolic process	78	320	1.950e-02
GO:BP	GO:0099111	microtubule-based transport	57	220	1.983e-02
GO:BP	GO:0042073	intraciliary transport	18	49	1.991e-02
GO:BP	GO:0034620	cellular response to unfolded protein	29	94	2.036e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	206	970	2.043e-02
GO:BP	GO:0016925	protein sumoylation	23	69	2.045e-02
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	47	174	2.055e-02
GO:BP	GO:0009134	nucleoside diphosphate catabolic process	32	107	2.057e-02
GO:BP	GO:0042325	regulation of phosphorylation	179	830	2.057e-02
GO:BP	GO:0030097	hemopoiesis	207	976	2.109e-02
GO:BP	GO:0048699	generation of neurons	313	1536	2.113e-02
GO:BP	GO:1990778	protein localization to cell periphery	87	365	2.119e-02
GO:BP	GO:0009179	purine ribonucleoside diphosphate metabolic process	34	116	2.138e-02
GO:BP	GO:0009135	purine nucleoside diphosphate metabolic process	34	116	2.138e-02
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	15	38	2.151e-02
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	31	103	2.151e-02
GO:BP	GO:0032869	cellular response to insulin stimulus	54	207	2.176e-02
GO:BP	GO:0072359	circulatory system development	239	1145	2.212e-02
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	11	24	2.307e-02
GO:BP	GO:0002320	lymphoid progenitor cell differentiation	11	24	2.307e-02
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	13	31	2.338e-02
GO:BP	GO:0030162	regulation of proteolysis	95	406	2.379e-02
GO:BP	GO:0042326	negative regulation of phosphorylation	65	260	2.409e-02
GO:BP	GO:0002183	cytoplasmic translational initiation	17	46	2.424e-02
GO:BP	GO:0042273	ribosomal large subunit biogenesis	23	70	2.459e-02
GO:BP	GO:0098813	nuclear chromosome segregation	78	323	2.462e-02
GO:BP	GO:0030307	positive regulation of cell growth	44	162	2.489e-02
GO:BP	GO:0071396	cellular response to lipid	136	613	2.500e-02
GO:BP	GO:0051099	positive regulation of binding	31	104	2.500e-02
GO:BP	GO:0006644	phospholipid metabolic process	92	392	2.512e-02
GO:BP	GO:1904263	positive regulation of TORC1 signaling	19	54	2.515e-02
GO:BP	GO:0060324	face development	19	54	2.515e-02
GO:BP	GO:0000018	regulation of DNA recombination	40	144	2.519e-02
GO:BP	GO:0098732	macromolecule deacylation	20	58	2.519e-02
GO:BP	GO:0010628	positive regulation of gene expression	251	1212	2.554e-02
GO:BP	GO:0009181	purine ribonucleoside diphosphate catabolic process	30	100	2.607e-02
GO:BP	GO:0009137	purine nucleoside diphosphate catabolic process	30	100	2.607e-02
GO:BP	GO:0051607	defense response to virus	77	319	2.609e-02
GO:BP	GO:0032886	regulation of microtubule-based process	66	266	2.639e-02
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	54	209	2.639e-02
GO:BP	GO:0003007	heart morphogenesis	66	266	2.639e-02
GO:BP	GO:0043065	positive regulation of apoptotic process	119	528	2.654e-02
GO:BP	GO:0034654	nucleobase-containing compound biosynthetic process	1312	7076	2.666e-02
GO:BP	GO:0097680	double-strand break repair via classical nonhomologous end joining	6	9	2.672e-02
GO:BP	GO:0031946	regulation of glucocorticoid biosynthetic process	6	9	2.672e-02
GO:BP	GO:0009138	pyrimidine nucleoside diphosphate metabolic process	6	9	2.672e-02
GO:BP	GO:0002009	morphogenesis of an epithelium	114	503	2.672e-02
GO:BP	GO:0007219	Notch signaling pathway	49	186	2.705e-02
GO:BP	GO:0002218	activation of innate immune response	74	305	2.705e-02
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	12	28	2.712e-02
GO:BP	GO:0060323	head morphogenesis	15	39	2.744e-02
GO:BP	GO:0070979	protein K11-linked ubiquitination	15	39	2.744e-02
GO:BP	GO:0032205	negative regulation of telomere maintenance	15	39	2.744e-02
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	34	118	2.744e-02
GO:BP	GO:0007507	heart development	134	605	2.753e-02
GO:BP	GO:0060485	mesenchyme development	77	320	2.769e-02
GO:BP	GO:0072659	protein localization to plasma membrane	71	291	2.804e-02
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	31	105	2.808e-02
GO:BP	GO:0015936	coenzyme A metabolic process	9	18	2.832e-02
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	54	210	2.854e-02
GO:BP	GO:0006360	transcription by RNA polymerase I	23	71	2.854e-02
GO:BP	GO:0046034	ATP metabolic process	58	229	2.875e-02
GO:BP	GO:0002831	regulation of response to biotic stimulus	121	540	2.915e-02
GO:BP	GO:0001841	neural tube formation	30	101	2.954e-02
GO:BP	GO:1900152	negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	7	12	2.985e-02
GO:BP	GO:0150011	regulation of neuron projection arborization	8	15	2.985e-02
GO:BP	GO:0002328	pro-B cell differentiation	7	12	2.985e-02
GO:BP	GO:0031126	sno(s)RNA 3’-end processing	7	12	2.985e-02
GO:BP	GO:0046463	acylglycerol biosynthetic process	18	51	2.985e-02
GO:BP	GO:0070243	regulation of thymocyte apoptotic process	8	15	2.985e-02
GO:BP	GO:0070986	left/right axis specification	8	15	2.985e-02
GO:BP	GO:0046460	neutral lipid biosynthetic process	18	51	2.985e-02
GO:BP	GO:0060211	regulation of nuclear-transcribed mRNA poly(A) tail shortening	8	15	2.985e-02
GO:BP	GO:0051081	nuclear membrane disassembly	7	12	2.985e-02
GO:BP	GO:0006220	pyrimidine nucleotide metabolic process	19	55	2.986e-02
GO:BP	GO:0043068	positive regulation of programmed cell death	122	546	3.038e-02
GO:BP	GO:2001251	negative regulation of chromosome organization	29	97	3.065e-02
GO:BP	GO:0032870	cellular response to hormone stimulus	140	638	3.072e-02
GO:BP	GO:0046039	GTP metabolic process	11	25	3.127e-02
GO:BP	GO:0008361	regulation of cell size	48	183	3.136e-02
GO:BP	GO:0035459	vesicle cargo loading	14	36	3.275e-02
GO:BP	GO:0016242	negative regulation of macroautophagy	14	36	3.275e-02
GO:BP	GO:0006779	porphyrin-containing compound biosynthetic process	14	36	3.275e-02
GO:BP	GO:0033014	tetrapyrrole biosynthetic process	14	36	3.275e-02
GO:BP	GO:0008286	insulin receptor signaling pathway	35	124	3.302e-02
GO:BP	GO:0001933	negative regulation of protein phosphorylation	61	245	3.303e-02
GO:BP	GO:0019218	regulation of steroid metabolic process	30	102	3.363e-02
GO:BP	GO:0048858	cell projection morphogenesis	148	681	3.397e-02
GO:BP	GO:0023052	signaling	1210	6515	3.400e-02
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	147	676	3.415e-02
GO:BP	GO:0030488	tRNA methylation	15	40	3.458e-02
GO:BP	GO:0072594	establishment of protein localization to organelle	144	661	3.494e-02
GO:BP	GO:0048598	embryonic morphogenesis	136	620	3.502e-02
GO:BP	GO:0035239	tube morphogenesis	186	879	3.529e-02
GO:BP	GO:0046785	microtubule polymerization	29	98	3.531e-02
GO:BP	GO:0090114	COPII-coated vesicle budding	16	44	3.574e-02
GO:BP	GO:0016601	Rac protein signal transduction	17	48	3.582e-02
GO:BP	GO:0046486	glycerolipid metabolic process	92	398	3.582e-02
GO:BP	GO:0030182	neuron differentiation	294	1451	3.582e-02
GO:BP	GO:0032211	negative regulation of telomere maintenance via telomerase	10	22	3.582e-02
GO:BP	GO:0048025	negative regulation of mRNA splicing, via spliceosome	10	22	3.582e-02
GO:BP	GO:0034315	regulation of Arp2/3 complex-mediated actin nucleation	12	29	3.582e-02
GO:BP	GO:0140861	DNA repair-dependent chromatin remodeling	10	22	3.582e-02
GO:BP	GO:0071763	nuclear membrane organization	17	48	3.582e-02
GO:BP	GO:0098534	centriole assembly	17	48	3.582e-02
GO:BP	GO:0060271	cilium assembly	93	403	3.582e-02
GO:BP	GO:0006513	protein monoubiquitination	17	48	3.582e-02
GO:BP	GO:0016032	viral process	97	423	3.582e-02
GO:BP	GO:0141137	positive regulation of gene expression, epigenetic	19	56	3.583e-02
GO:BP	GO:0030520	estrogen receptor signaling pathway	18	52	3.595e-02
GO:BP	GO:0014020	primary neural tube formation	28	94	3.654e-02
GO:BP	GO:0035295	tube development	228	1101	3.654e-02
GO:BP	GO:0045862	positive regulation of proteolysis	55	218	3.753e-02
GO:BP	GO:0009247	glycolipid biosynthetic process	24	77	3.759e-02
GO:BP	GO:0045088	regulation of innate immune response	102	449	3.785e-02
GO:BP	GO:0097581	lamellipodium organization	27	90	3.846e-02
GO:BP	GO:0046488	phosphatidylinositol metabolic process	43	162	3.880e-02
GO:BP	GO:0005975	carbohydrate metabolic process	124	561	3.894e-02
GO:BP	GO:0009218	pyrimidine ribonucleotide metabolic process	13	33	3.894e-02
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	23	73	3.894e-02
GO:BP	GO:0048869	cellular developmental process	838	4438	3.915e-02
GO:BP	GO:0040031	snRNA modification	5	7	3.944e-02
GO:BP	GO:0007221	positive regulation of transcription of Notch receptor target	5	7	3.944e-02
GO:BP	GO:0046048	UDP metabolic process	5	7	3.944e-02
GO:BP	GO:2000064	regulation of cortisol biosynthetic process	5	7	3.944e-02
GO:BP	GO:0009193	pyrimidine ribonucleoside diphosphate metabolic process	5	7	3.944e-02
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	29	99	3.944e-02
GO:BP	GO:0051204	protein insertion into mitochondrial membrane	5	7	3.944e-02
GO:BP	GO:0032459	regulation of protein oligomerization	5	7	3.944e-02
GO:BP	GO:0019364	pyridine nucleotide catabolic process	29	99	3.944e-02
GO:BP	GO:0002084	protein depalmitoylation	5	7	3.944e-02
GO:BP	GO:0006370	7-methylguanosine mRNA capping	5	7	3.944e-02
GO:BP	GO:0060627	regulation of vesicle-mediated transport	118	531	3.955e-02
GO:BP	GO:0051348	negative regulation of transferase activity	44	167	3.955e-02
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	88	380	3.973e-02
GO:BP	GO:0035282	segmentation	31	108	4.019e-02
GO:BP	GO:0051650	establishment of vesicle localization	51	200	4.019e-02
GO:BP	GO:2000765	regulation of cytoplasmic translation	14	37	4.064e-02
GO:BP	GO:0051656	establishment of organelle localization	110	491	4.090e-02
GO:BP	GO:0001932	regulation of protein phosphorylation	166	779	4.116e-02
GO:BP	GO:0046339	diacylglycerol metabolic process	11	26	4.137e-02
GO:BP	GO:0006352	DNA-templated transcription initiation	53	210	4.214e-02
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	15	41	4.214e-02
GO:BP	GO:0141085	regulation of inflammasome-mediated signaling pathway	15	41	4.214e-02
GO:BP	GO:0030154	cell differentiation	837	4437	4.217e-02
GO:BP	GO:1901699	cellular response to nitrogen compound	140	645	4.225e-02
GO:BP	GO:0046031	ADP metabolic process	30	104	4.236e-02
GO:BP	GO:0051055	negative regulation of lipid biosynthetic process	19	57	4.241e-02
GO:BP	GO:0030490	maturation of SSU-rRNA	18	53	4.292e-02
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	32	113	4.292e-02
GO:BP	GO:0050810	regulation of steroid biosynthetic process	24	78	4.292e-02
GO:BP	GO:2000785	regulation of autophagosome assembly	17	49	4.300e-02
GO:BP	GO:0016074	sno(s)RNA metabolic process	8	16	4.451e-02
GO:BP	GO:0042795	snRNA transcription by RNA polymerase II	8	16	4.451e-02
GO:BP	GO:0032940	secretion by cell	180	854	4.460e-02
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	37	136	4.499e-02
GO:BP	GO:0035050	embryonic heart tube development	26	87	4.562e-02
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	12	30	4.593e-02
GO:BP	GO:0006091	generation of precursor metabolites and energy	107	478	4.618e-02
GO:BP	GO:1990144	intrinsic apoptotic signaling pathway in response to hypoxia	6	10	4.697e-02
GO:BP	GO:0070244	negative regulation of thymocyte apoptotic process	6	10	4.697e-02
GO:BP	GO:0071600	otic vesicle morphogenesis	6	10	4.697e-02
GO:BP	GO:0071166	ribonucleoprotein complex localization	6	10	4.697e-02
GO:BP	GO:0015937	coenzyme A biosynthetic process	6	10	4.697e-02
GO:BP	GO:0016559	peroxisome fission	6	10	4.697e-02
GO:BP	GO:0034551	mitochondrial respiratory chain complex III assembly	7	13	4.724e-02
GO:BP	GO:0030397	membrane disassembly	7	13	4.724e-02
GO:BP	GO:1902902	negative regulation of autophagosome assembly	7	13	4.724e-02
GO:BP	GO:0017062	respiratory chain complex III assembly	7	13	4.724e-02
GO:BP	GO:0006446	regulation of translational initiation	25	83	4.745e-02
GO:BP	GO:0043413	macromolecule glycosylation	56	226	4.799e-02
GO:BP	GO:0007265	Ras protein signal transduction	34	123	4.799e-02
GO:BP	GO:0006486	protein glycosylation	56	226	4.799e-02
GO:BP	GO:0050686	negative regulation of mRNA processing	10	23	4.819e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	429	2192	4.843e-02
GO:BP	GO:0045010	actin nucleation	20	62	4.914e-02
GO:BP	GO:0006611	protein export from nucleus	20	62	4.914e-02
GO:BP	GO:0032273	positive regulation of protein polymerization	27	92	4.932e-02
GO:BP	GO:0031667	response to nutrient levels	113	510	4.965e-02
KEGG	KEGG:05168	Herpes simplex virus 1 infection	161	506	1.414e-08
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	45	140	2.768e-02
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	52	168	2.768e-02
KEGG	KEGG:03083	Polycomb repressive complex	31	84	2.768e-02
KEGG	KEGG:03013	Nucleocytoplasmic transport	37	108	2.768e-02
KEGG	KEGG:00510	N-Glycan biosynthesis	21	53	4.247e-02
KEGG	KEGG:03018	RNA degradation	28	79	4.383e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	96	363	4.737e-02
KEGG	KEGG:04137	Mitophagy - animal	34	103	4.737e-02
KEGG	KEGG:03082	ATP-dependent chromatin remodeling	37	116	4.974e-02

write.csv(table_DOX24_genes, "output/table_DOX24_genes.csv")

#GO:BP
table_DOX24_genes_GOBP <- table_DOX24_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))


table_DOX24_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24_genes_KEGG <- table_DOX24_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX24T shared DEGs GO KEGG#####
D24Tshare_DEGs_mat <- as.matrix(DOX24T_share_DEGs_GO_plot)

DOX_24Tshare_dxr_gene <- gost(query = D24Tshare_DEGs_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24Tshare_gost_genes <- gostplot(DOX_24Tshare_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24Tshare_gost_genes

table_DOX24Tshare_genes <- DOX_24Tshare_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24Tshare_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	2739	5390	1.755e-121
GO:BP	GO:0006996	organelle organization	1921	3594	2.051e-102
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	2049	3990	1.355e-88
GO:BP	GO:0048522	positive regulation of cellular process	2841	5920	2.002e-87
GO:BP	GO:0019538	protein metabolic process	2351	4721	2.002e-87
GO:BP	GO:0048518	positive regulation of biological process	2973	6264	7.043e-86
GO:BP	GO:0065007	biological regulation	5395	12743	3.303e-81
GO:BP	GO:0051252	regulation of RNA metabolic process	1888	3687	5.607e-79
GO:BP	GO:0050789	regulation of biological process	5240	12336	6.328e-79
GO:BP	GO:0050794	regulation of cellular process	5082	11946	9.851e-75
GO:BP	GO:0006351	DNA-templated transcription	1811	3549	1.456e-73
GO:BP	GO:0043412	macromolecule modification	1586	3030	6.777e-73
GO:BP	GO:0009056	catabolic process	1403	2639	7.203e-69
GO:BP	GO:0006355	regulation of DNA-templated transcription	1729	3409	5.092e-67
GO:BP	GO:2001141	regulation of RNA biosynthetic process	1735	3428	1.890e-66
GO:BP	GO:0051641	cellular localization	1829	3661	3.225e-65
GO:BP	GO:0033554	cellular response to stress	1029	1830	1.246e-64
GO:BP	GO:0051128	regulation of cellular component organization	1294	2433	5.635e-63
GO:BP	GO:0019222	regulation of metabolic process	3177	7035	7.511e-62
GO:BP	GO:0035556	intracellular signal transduction	1519	2965	3.462e-61
GO:BP	GO:0009893	positive regulation of metabolic process	1784	3597	2.344e-60
GO:BP	GO:0036211	protein modification process	1462	2846	1.701e-59
GO:BP	GO:0051179	localization	2578	5555	1.049e-58
GO:BP	GO:0051649	establishment of localization in cell	1091	2010	5.894e-58
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	1636	3288	1.444e-55
GO:BP	GO:0033036	macromolecule localization	1603	3228	1.599e-53
GO:BP	GO:0046907	intracellular transport	790	1381	1.415e-52
GO:BP	GO:0060255	regulation of macromolecule metabolic process	2912	6492	8.338e-51
GO:BP	GO:0006366	transcription by RNA polymerase II	1369	2711	1.330e-49
GO:BP	GO:0070727	cellular macromolecule localization	1397	2782	5.358e-49
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	1074	2036	7.468e-49
GO:BP	GO:0008104	protein localization	1388	2770	5.618e-48
GO:BP	GO:0009057	macromolecule catabolic process	791	1417	6.371e-47
GO:BP	GO:0033043	regulation of organelle organization	666	1148	1.055e-46
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	1300	2578	2.341e-46
GO:BP	GO:0007049	cell cycle	897	1663	3.176e-45
GO:BP	GO:0009894	regulation of catabolic process	610	1040	1.127e-44
GO:BP	GO:0023051	regulation of signaling	1668	3478	7.507e-44
GO:BP	GO:0006810	transport	2047	4407	1.218e-43
GO:BP	GO:0010646	regulation of cell communication	1669	3486	2.465e-43
GO:BP	GO:0000278	mitotic cell cycle	536	892	2.989e-43
GO:BP	GO:0007275	multicellular organism development	2170	4727	2.067e-42
GO:BP	GO:0051254	positive regulation of RNA metabolic process	963	1835	4.114e-42
GO:BP	GO:0009966	regulation of signal transduction	1475	3034	6.247e-42
GO:BP	GO:0006796	phosphate-containing compound metabolic process	1210	2407	6.374e-42
GO:BP	GO:0006974	DNA damage response	540	908	9.179e-42
GO:BP	GO:0006793	phosphorus metabolic process	1210	2410	1.335e-41
GO:BP	GO:0032502	developmental process	2879	6553	4.545e-40
GO:BP	GO:1903047	mitotic cell cycle process	455	745	5.526e-39
GO:BP	GO:0051726	regulation of cell cycle	614	1087	5.990e-38
GO:BP	GO:0048856	anatomical structure development	2649	5997	9.026e-38
GO:BP	GO:0015031	protein transport	775	1444	1.212e-37
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	887	1699	2.203e-37
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	886	1697	2.347e-37
GO:BP	GO:0051234	establishment of localization	2223	4928	4.152e-37
GO:BP	GO:0071705	nitrogen compound transport	983	1923	6.126e-37
GO:BP	GO:0048583	regulation of response to stimulus	1846	3993	7.522e-37
GO:BP	GO:0051246	regulation of protein metabolic process	953	1855	8.137e-37
GO:BP	GO:0061919	process utilizing autophagic mechanism	377	597	1.222e-36
GO:BP	GO:0006914	autophagy	377	597	1.222e-36
GO:BP	GO:0022402	cell cycle process	696	1280	5.677e-36
GO:BP	GO:0048523	negative regulation of cellular process	2494	5629	5.755e-36
GO:BP	GO:0051716	cellular response to stimulus	3171	7376	1.258e-35
GO:BP	GO:0006259	DNA metabolic process	569	1005	1.776e-35
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	1257	2593	3.510e-34
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	800	1529	6.884e-34
GO:BP	GO:0009891	positive regulation of biosynthetic process	1298	2696	1.027e-33
GO:BP	GO:0048731	system development	1854	4053	1.078e-33
GO:BP	GO:0048519	negative regulation of biological process	2560	5834	1.769e-33
GO:BP	GO:0070925	organelle assembly	582	1046	1.962e-33
GO:BP	GO:0044238	primary metabolic process	5009	12342	6.407e-33
GO:BP	GO:0030163	protein catabolic process	573	1030	7.242e-33
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	391	643	8.187e-33
GO:BP	GO:1902531	regulation of intracellular signal transduction	979	1953	1.470e-32
GO:BP	GO:0009889	regulation of biosynthetic process	2544	5809	1.853e-32
GO:BP	GO:0019941	modification-dependent protein catabolic process	386	638	1.019e-31
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	455	786	4.093e-31
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	2471	5644	4.538e-31
GO:BP	GO:0043687	post-translational protein modification	565	1027	1.187e-30
GO:BP	GO:0051253	negative regulation of RNA metabolic process	731	1400	1.994e-30
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	378	628	2.141e-30
GO:BP	GO:0006281	DNA repair	372	621	2.689e-29
GO:BP	GO:0016236	macroautophagy	242	362	1.151e-28
GO:BP	GO:0006325	chromatin organization	493	884	2.029e-28
GO:BP	GO:0006950	response to stress	1783	3948	2.030e-28
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	533	975	6.447e-28
GO:BP	GO:0010468	regulation of gene expression	2405	5536	2.817e-27
GO:BP	GO:0032446	protein modification by small protein conjugation	475	853	3.822e-27
GO:BP	GO:0007399	nervous system development	1229	2604	3.822e-27
GO:BP	GO:0009896	positive regulation of catabolic process	329	546	1.868e-26
GO:BP	GO:0010564	regulation of cell cycle process	411	720	2.853e-26
GO:BP	GO:0008219	cell death	968	1991	4.529e-26
GO:BP	GO:0012501	programmed cell death	966	1987	5.279e-26
GO:BP	GO:0140053	mitochondrial gene expression	132	168	5.667e-26
GO:BP	GO:0030030	cell projection organization	814	1631	7.268e-26
GO:BP	GO:0032879	regulation of localization	982	2029	1.237e-25
GO:BP	GO:0006915	apoptotic process	937	1923	1.434e-25
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	660	1280	2.341e-25
GO:BP	GO:0050793	regulation of developmental process	1159	2457	2.658e-25
GO:BP	GO:0141124	intracellular signaling cassette	930	1912	4.802e-25
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	665	1296	7.932e-25
GO:BP	GO:0009653	anatomical structure morphogenesis	1262	2713	8.379e-25
GO:BP	GO:0010498	proteasomal protein catabolic process	323	543	1.273e-24
GO:BP	GO:0045184	establishment of protein localization	938	1937	1.732e-24
GO:BP	GO:0071840	cellular component organization or biogenesis	3483	8393	1.767e-24
GO:BP	GO:0016192	vesicle-mediated transport	791	1592	2.298e-24
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	789	1588	2.676e-24
GO:BP	GO:0007346	regulation of mitotic cell cycle	297	492	4.876e-24
GO:BP	GO:0044087	regulation of cellular component biogenesis	536	1011	6.641e-24
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	258	414	1.178e-23
GO:BP	GO:0009968	negative regulation of signal transduction	673	1326	1.580e-23
GO:BP	GO:0051276	chromosome organization	332	574	2.071e-22
GO:BP	GO:0016567	protein ubiquitination	421	768	3.624e-22
GO:BP	GO:0009987	cellular process	7650	20247	3.878e-22
GO:BP	GO:0050896	response to stimulus	3692	8999	5.790e-22
GO:BP	GO:0060341	regulation of cellular localization	530	1013	6.326e-22
GO:BP	GO:0006412	translation	401	727	9.396e-22
GO:BP	GO:0010648	negative regulation of cell communication	713	1436	1.072e-21
GO:BP	GO:0023057	negative regulation of signaling	712	1435	1.459e-21
GO:BP	GO:0044772	mitotic cell cycle phase transition	260	428	1.543e-21
GO:BP	GO:0051640	organelle localization	351	620	1.602e-21
GO:BP	GO:1903311	regulation of mRNA metabolic process	202	312	2.618e-21
GO:BP	GO:0032880	regulation of protein localization	480	907	4.260e-21
GO:BP	GO:0065009	regulation of molecular function	736	1496	4.303e-21
GO:BP	GO:0048468	cell development	1308	2876	4.348e-21
GO:BP	GO:0007010	cytoskeleton organization	750	1529	4.348e-21
GO:BP	GO:0019637	organophosphate metabolic process	555	1077	4.422e-21
GO:BP	GO:0044770	cell cycle phase transition	308	532	7.178e-21
GO:BP	GO:0006338	chromatin remodeling	397	725	8.823e-21
GO:BP	GO:0032543	mitochondrial translation	103	130	9.395e-21
GO:BP	GO:0048869	cellular developmental process	1928	4438	1.751e-20
GO:BP	GO:0010638	positive regulation of organelle organization	288	492	1.819e-20
GO:BP	GO:0030154	cell differentiation	1927	4437	2.116e-20
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	630	1256	2.252e-20
GO:BP	GO:0016310	phosphorylation	657	1320	3.034e-20
GO:BP	GO:0022008	neurogenesis	848	1771	3.387e-20
GO:BP	GO:0080135	regulation of cellular response to stress	300	519	3.435e-20
GO:BP	GO:0051129	negative regulation of cellular component organization	384	701	3.902e-20
GO:BP	GO:0006886	intracellular protein transport	377	686	4.383e-20
GO:BP	GO:0023052	signaling	2731	6515	6.831e-20
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	365	662	9.512e-20
GO:BP	GO:0051130	positive regulation of cellular component organization	562	1105	9.656e-20
GO:BP	GO:0043009	chordate embryonic development	369	671	1.020e-19
GO:BP	GO:0048585	negative regulation of response to stimulus	807	1680	1.258e-19
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	378	692	1.537e-19
GO:BP	GO:0044281	small molecule metabolic process	846	1776	2.271e-19
GO:BP	GO:0140014	mitotic nuclear division	182	282	5.437e-19
GO:BP	GO:0007005	mitochondrion organization	257	435	5.437e-19
GO:BP	GO:0010506	regulation of autophagy	224	367	6.527e-19
GO:BP	GO:0007154	cell communication	2732	6540	7.798e-19
GO:BP	GO:0042254	ribosome biogenesis	202	323	9.484e-19
GO:BP	GO:0009790	embryo development	571	1135	9.485e-19
GO:BP	GO:0051301	cell division	360	658	9.588e-19
GO:BP	GO:0051052	regulation of DNA metabolic process	287	500	1.005e-18
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	485	938	1.005e-18
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	303	535	1.330e-18
GO:BP	GO:0016072	rRNA metabolic process	173	266	1.422e-18
GO:BP	GO:0032259	methylation	157	236	2.985e-18
GO:BP	GO:0016043	cellular component organization	3353	8184	3.034e-18
GO:BP	GO:0065008	regulation of biological quality	1319	2947	3.315e-18
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	202	327	6.990e-18
GO:BP	GO:0006302	double-strand break repair	198	319	7.401e-18
GO:BP	GO:1901987	regulation of cell cycle phase transition	250	427	8.915e-18
GO:BP	GO:0033044	regulation of chromosome organization	159	242	1.074e-17
GO:BP	GO:0031399	regulation of protein modification process	529	1049	1.369e-17
GO:BP	GO:0016197	endosomal transport	183	290	1.399e-17
GO:BP	GO:0061024	membrane organization	429	821	1.526e-17
GO:BP	GO:0006399	tRNA metabolic process	142	210	1.828e-17
GO:BP	GO:1901135	carbohydrate derivative metabolic process	499	983	2.929e-17
GO:BP	GO:0048699	generation of neurons	734	1536	4.627e-17
GO:BP	GO:0010639	negative regulation of organelle organization	212	352	5.807e-17
GO:BP	GO:0051247	positive regulation of protein metabolic process	522	1039	6.083e-17
GO:BP	GO:0006468	protein phosphorylation	602	1227	8.911e-17
GO:BP	GO:0043484	regulation of RNA splicing	128	187	2.163e-16
GO:BP	GO:0042981	regulation of apoptotic process	699	1462	2.945e-16
GO:BP	GO:0000819	sister chromatid segregation	152	234	3.118e-16
GO:BP	GO:0000226	microtubule cytoskeleton organization	357	670	3.416e-16
GO:BP	GO:0001701	in utero embryonic development	239	413	3.859e-16
GO:BP	GO:0043414	macromolecule methylation	95	127	3.859e-16
GO:BP	GO:0042176	regulation of protein catabolic process	218	369	4.244e-16
GO:BP	GO:0051656	establishment of organelle localization	275	491	5.285e-16
GO:BP	GO:0043067	regulation of programmed cell death	716	1506	5.609e-16
GO:BP	GO:0006403	RNA localization	134	200	5.740e-16
GO:BP	GO:0006402	mRNA catabolic process	165	261	5.844e-16
GO:BP	GO:0071495	cellular response to endogenous stimulus	596	1223	7.720e-16
GO:BP	GO:0007017	microtubule-based process	500	999	8.098e-16
GO:BP	GO:0000070	mitotic sister chromatid segregation	129	193	3.097e-15
GO:BP	GO:0072359	circulatory system development	560	1145	3.216e-15
GO:BP	GO:0007059	chromosome segregation	243	427	3.216e-15
GO:BP	GO:0030182	neuron differentiation	689	1451	3.417e-15
GO:BP	GO:0140694	membraneless organelle assembly	244	430	4.415e-15
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	145	225	4.696e-15
GO:BP	GO:0006364	rRNA processing	145	225	4.696e-15
GO:BP	GO:0045786	negative regulation of cell cycle	219	377	4.847e-15
GO:BP	GO:0048285	organelle fission	276	500	5.622e-15
GO:BP	GO:0007165	signal transduction	2491	6002	7.400e-15
GO:BP	GO:0016055	Wnt signaling pathway	256	458	9.460e-15
GO:BP	GO:0009967	positive regulation of signal transduction	739	1578	1.229e-14
GO:BP	GO:0009719	response to endogenous stimulus	701	1489	1.893e-14
GO:BP	GO:0080134	regulation of response to stress	658	1387	2.272e-14
GO:BP	GO:0050790	regulation of catalytic activity	463	928	2.597e-14
GO:BP	GO:0006508	proteolysis	699	1486	2.605e-14
GO:BP	GO:0000075	cell cycle checkpoint signaling	123	185	2.844e-14
GO:BP	GO:0000902	cell morphogenesis	492	996	2.906e-14
GO:BP	GO:0007264	small GTPase-mediated signal transduction	276	505	2.958e-14
GO:BP	GO:0006417	regulation of translation	218	380	3.642e-14
GO:BP	GO:0031175	neuron projection development	503	1023	3.848e-14
GO:BP	GO:0044093	positive regulation of molecular function	443	884	4.385e-14
GO:BP	GO:0051169	nuclear transport	196	334	4.507e-14
GO:BP	GO:0006913	nucleocytoplasmic transport	196	334	4.507e-14
GO:BP	GO:0007507	heart development	320	605	6.128e-14
GO:BP	GO:0048666	neuron development	567	1177	7.747e-14
GO:BP	GO:0098813	nuclear chromosome segregation	190	323	8.822e-14
GO:BP	GO:0051049	regulation of transport	746	1607	9.732e-14
GO:BP	GO:0033365	protein localization to organelle	580	1209	9.732e-14
GO:BP	GO:0006401	RNA catabolic process	186	315	1.027e-13
GO:BP	GO:0051094	positive regulation of developmental process	636	1343	1.084e-13
GO:BP	GO:0007033	vacuole organization	149	239	1.108e-13
GO:BP	GO:0009628	response to abiotic stimulus	552	1144	1.253e-13
GO:BP	GO:0022411	cellular component disassembly	247	446	1.254e-13
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	96	136	1.254e-13
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	418	831	1.311e-13
GO:BP	GO:0010948	negative regulation of cell cycle process	173	289	1.618e-13
GO:BP	GO:0000045	autophagosome assembly	86	118	1.638e-13
GO:BP	GO:0000280	nuclear division	249	452	2.180e-13
GO:BP	GO:0006753	nucleoside phosphate metabolic process	336	646	2.422e-13
GO:BP	GO:0008033	tRNA processing	97	139	2.849e-13
GO:BP	GO:0141188	nucleic acid catabolic process	198	343	3.032e-13
GO:BP	GO:0010256	endomembrane system organization	321	613	3.046e-13
GO:BP	GO:0048584	positive regulation of response to stimulus	1038	2331	3.180e-13
GO:BP	GO:0045595	regulation of cell differentiation	730	1576	3.444e-13
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	347	673	4.159e-13
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	475	970	5.562e-13
GO:BP	GO:0051493	regulation of cytoskeleton organization	277	517	6.198e-13
GO:BP	GO:0051248	negative regulation of protein metabolic process	348	677	6.533e-13
GO:BP	GO:0023056	positive regulation of signaling	818	1796	8.763e-13
GO:BP	GO:0031344	regulation of cell projection organization	339	658	9.641e-13
GO:BP	GO:0000723	telomere maintenance	109	164	1.165e-12
GO:BP	GO:0060562	epithelial tube morphogenesis	193	336	1.242e-12
GO:BP	GO:0008152	metabolic process	5499	14136	1.249e-12
GO:BP	GO:0030029	actin filament-based process	411	825	1.409e-12
GO:BP	GO:0090407	organophosphate biosynthetic process	321	619	1.565e-12
GO:BP	GO:0000209	protein polyubiquitination	166	280	1.809e-12
GO:BP	GO:0018193	peptidyl-amino acid modification	350	686	2.027e-12
GO:BP	GO:1905037	autophagosome organization	88	125	2.120e-12
GO:BP	GO:0035239	tube morphogenesis	433	879	2.636e-12
GO:BP	GO:0006260	DNA replication	167	283	2.653e-12
GO:BP	GO:0051239	regulation of multicellular organismal process	1281	2956	2.854e-12
GO:BP	GO:0010647	positive regulation of cell communication	814	1795	3.273e-12
GO:BP	GO:0061061	muscle structure development	352	693	3.688e-12
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	178	307	3.732e-12
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	311	600	4.121e-12
GO:BP	GO:1903829	positive regulation of protein localization	266	499	4.250e-12
GO:BP	GO:0006839	mitochondrial transport	115	178	4.308e-12
GO:BP	GO:0016241	regulation of macroautophagy	118	184	4.448e-12
GO:BP	GO:0032501	multicellular organismal process	2967	7322	4.478e-12
GO:BP	GO:0009895	negative regulation of catabolic process	203	361	4.552e-12
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	329	642	5.400e-12
GO:BP	GO:0030031	cell projection assembly	316	613	6.303e-12
GO:BP	GO:0051236	establishment of RNA localization	107	163	6.422e-12
GO:BP	GO:0070848	response to growth factor	363	721	6.979e-12
GO:BP	GO:0042770	signal transduction in response to DNA damage	112	173	7.127e-12
GO:BP	GO:0035295	tube development	525	1101	7.169e-12
GO:BP	GO:0071363	cellular response to growth factor stimulus	349	689	7.256e-12
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	149	248	7.481e-12
GO:BP	GO:0048513	animal organ development	1328	3085	9.127e-12
GO:BP	GO:0009117	nucleotide metabolic process	262	493	9.802e-12
GO:BP	GO:0051054	positive regulation of DNA metabolic process	169	291	1.221e-11
GO:BP	GO:0009451	RNA modification	112	174	1.238e-11
GO:BP	GO:0061013	regulation of mRNA catabolic process	124	198	1.254e-11
GO:BP	GO:0060537	muscle tissue development	233	430	1.468e-11
GO:BP	GO:0014706	striated muscle tissue development	223	408	1.468e-11
GO:BP	GO:0006282	regulation of DNA repair	137	225	1.642e-11
GO:BP	GO:1990778	protein localization to cell periphery	203	365	1.827e-11
GO:BP	GO:0044782	cilium organization	233	431	2.008e-11
GO:BP	GO:0006400	tRNA modification	70	95	2.060e-11
GO:BP	GO:0051168	nuclear export	109	169	2.060e-11
GO:BP	GO:0009267	cellular response to starvation	113	177	2.129e-11
GO:BP	GO:1902115	regulation of organelle assembly	141	234	2.308e-11
GO:BP	GO:0043065	positive regulation of apoptotic process	276	528	2.696e-11
GO:BP	GO:1901698	response to nitrogen compound	513	1080	2.903e-11
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	87	127	3.057e-11
GO:BP	GO:0050658	RNA transport	104	160	3.309e-11
GO:BP	GO:0050657	nucleic acid transport	104	160	3.309e-11
GO:BP	GO:0006360	transcription by RNA polymerase I	56	71	3.486e-11
GO:BP	GO:0031647	regulation of protein stability	188	335	4.292e-11
GO:BP	GO:0045017	glycerolipid biosynthetic process	148	250	4.340e-11
GO:BP	GO:0043068	positive regulation of programmed cell death	283	546	4.839e-11
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	141	236	5.583e-11
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	201	364	5.619e-11
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	122	197	5.619e-11
GO:BP	GO:0050684	regulation of mRNA processing	90	134	6.939e-11
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	108	170	1.044e-10
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	109	172	1.044e-10
GO:BP	GO:0042592	homeostatic process	780	1736	1.085e-10
GO:BP	GO:0042594	response to starvation	132	219	1.158e-10
GO:BP	GO:0034330	cell junction organization	406	834	1.187e-10
GO:BP	GO:0048193	Golgi vesicle transport	176	312	1.193e-10
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	127	209	1.316e-10
GO:BP	GO:0045732	positive regulation of protein catabolic process	127	209	1.316e-10
GO:BP	GO:0008654	phospholipid biosynthetic process	150	257	1.380e-10
GO:BP	GO:0048738	cardiac muscle tissue development	139	234	1.410e-10
GO:BP	GO:0048858	cell projection morphogenesis	340	681	1.431e-10
GO:BP	GO:0032200	telomere organization	118	191	1.578e-10
GO:BP	GO:0060070	canonical Wnt signaling pathway	175	311	1.792e-10
GO:BP	GO:0009892	negative regulation of metabolic process	1431	3375	1.852e-10
GO:BP	GO:0009888	tissue development	898	2032	1.854e-10
GO:BP	GO:0051174	regulation of phosphorus metabolic process	457	957	1.919e-10
GO:BP	GO:0008610	lipid biosynthetic process	360	729	2.018e-10
GO:BP	GO:0015931	nucleobase-containing compound transport	140	237	2.052e-10
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	337	676	2.210e-10
GO:BP	GO:0006354	DNA-templated transcription elongation	89	134	2.245e-10
GO:BP	GO:0019220	regulation of phosphate metabolic process	456	956	2.471e-10
GO:BP	GO:0010970	transport along microtubule	111	178	2.806e-10
GO:BP	GO:0002009	morphogenesis of an epithelium	261	503	2.887e-10
GO:BP	GO:0007166	cell surface receptor signaling pathway	1210	2819	3.111e-10
GO:BP	GO:0032984	protein-containing complex disassembly	149	257	3.149e-10
GO:BP	GO:0016050	vesicle organization	204	376	3.189e-10
GO:BP	GO:0042325	regulation of phosphorylation	402	830	3.455e-10
GO:BP	GO:0060271	cilium assembly	216	403	3.676e-10
GO:BP	GO:0006163	purine nucleotide metabolic process	228	430	3.996e-10
GO:BP	GO:0043487	regulation of RNA stability	118	193	4.016e-10
GO:BP	GO:0048729	tissue morphogenesis	309	614	4.043e-10
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	91	139	4.275e-10
GO:BP	GO:0043488	regulation of mRNA stability	112	181	4.468e-10
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	106	169	4.758e-10
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	300	594	4.758e-10
GO:BP	GO:0040007	growth	443	929	5.025e-10
GO:BP	GO:0097190	apoptotic signaling pathway	305	606	5.342e-10
GO:BP	GO:0006310	DNA recombination	190	347	5.510e-10
GO:BP	GO:0038202	TORC1 signaling	72	103	5.513e-10
GO:BP	GO:0072521	purine-containing compound metabolic process	286	563	6.207e-10
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	40	47	6.249e-10
GO:BP	GO:0051028	mRNA transport	86	130	6.582e-10
GO:BP	GO:2000026	regulation of multicellular organismal development	645	1418	6.703e-10
GO:BP	GO:1902903	regulation of supramolecular fiber organization	206	383	6.922e-10
GO:BP	GO:0006383	transcription by RNA polymerase III	49	62	7.070e-10
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	103	164	7.976e-10
GO:BP	GO:0044839	cell cycle G2/M phase transition	99	156	8.036e-10
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	260	505	8.556e-10
GO:BP	GO:0030036	actin cytoskeleton organization	357	729	8.693e-10
GO:BP	GO:0000725	recombinational repair	117	193	1.015e-09
GO:BP	GO:0048812	neuron projection morphogenesis	327	660	1.070e-09
GO:BP	GO:0042692	muscle cell differentiation	215	405	1.251e-09
GO:BP	GO:0032204	regulation of telomere maintenance	76	112	1.456e-09
GO:BP	GO:0070201	regulation of establishment of protein localization	273	537	1.555e-09
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	187	344	1.730e-09
GO:BP	GO:0000724	double-strand break repair via homologous recombination	114	188	1.742e-09
GO:BP	GO:0031503	protein-containing complex localization	127	215	1.758e-09
GO:BP	GO:0030111	regulation of Wnt signaling pathway	181	331	1.820e-09
GO:BP	GO:0006629	lipid metabolic process	631	1391	1.931e-09
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	85	130	2.063e-09
GO:BP	GO:0071897	DNA biosynthetic process	106	172	2.063e-09
GO:BP	GO:0016073	snRNA metabolic process	46	58	2.252e-09
GO:BP	GO:0006644	phospholipid metabolic process	208	392	2.670e-09
GO:BP	GO:0070887	cellular response to chemical stimulus	953	2192	2.831e-09
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	124	210	2.998e-09
GO:BP	GO:0043085	positive regulation of catalytic activity	279	554	3.372e-09
GO:BP	GO:0031929	TOR signaling	103	167	3.533e-09
GO:BP	GO:1901699	cellular response to nitrogen compound	318	645	3.930e-09
GO:BP	GO:0010975	regulation of neuron projection development	231	446	5.066e-09
GO:BP	GO:0007006	mitochondrial membrane organization	77	116	5.363e-09
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	78	118	5.545e-09
GO:BP	GO:2001251	negative regulation of chromosome organization	67	97	5.877e-09
GO:BP	GO:0072331	signal transduction by p53 class mediator	101	164	5.943e-09
GO:BP	GO:0006261	DNA-templated DNA replication	99	160	6.135e-09
GO:BP	GO:0031669	cellular response to nutrient levels	141	248	6.616e-09
GO:BP	GO:0006650	glycerophospholipid metabolic process	169	309	7.354e-09
GO:BP	GO:0051604	protein maturation	271	539	7.549e-09
GO:BP	GO:0034976	response to endoplasmic reticulum stress	151	270	7.844e-09
GO:BP	GO:0040008	regulation of growth	299	604	7.894e-09
GO:BP	GO:0031400	negative regulation of protein modification process	187	349	8.006e-09
GO:BP	GO:0003007	heart morphogenesis	149	266	8.754e-09
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	548	1199	9.123e-09
GO:BP	GO:0001510	RNA methylation	58	81	1.026e-08
GO:BP	GO:0010212	response to ionizing radiation	89	141	1.110e-08
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	31	35	1.359e-08
GO:BP	GO:0051338	regulation of transferase activity	252	498	1.428e-08
GO:BP	GO:0019693	ribose phosphate metabolic process	200	380	1.436e-08
GO:BP	GO:0046486	glycerolipid metabolic process	208	398	1.442e-08
GO:BP	GO:0045597	positive regulation of cell differentiation	414	879	1.592e-08
GO:BP	GO:0001932	regulation of protein phosphorylation	372	779	1.600e-08
GO:BP	GO:0000077	DNA damage checkpoint signaling	75	114	1.642e-08
GO:BP	GO:0016049	cell growth	246	485	1.700e-08
GO:BP	GO:0008283	cell population proliferation	876	2015	1.754e-08
GO:BP	GO:0032386	regulation of intracellular transport	148	266	1.849e-08
GO:BP	GO:0009259	ribonucleotide metabolic process	196	372	1.861e-08
GO:BP	GO:0070585	protein localization to mitochondrion	84	132	1.861e-08
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	295	599	1.994e-08
GO:BP	GO:0104004	cellular response to environmental stimulus	181	339	2.136e-08
GO:BP	GO:0071214	cellular response to abiotic stimulus	181	339	2.136e-08
GO:BP	GO:2001252	positive regulation of chromosome organization	70	105	2.505e-08
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	70	105	2.505e-08
GO:BP	GO:0010508	positive regulation of autophagy	98	161	2.560e-08
GO:BP	GO:0035966	response to topologically incorrect protein	96	157	2.679e-08
GO:BP	GO:0097435	supramolecular fiber organization	405	861	2.910e-08
GO:BP	GO:0099111	microtubule-based transport	126	220	2.957e-08
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	79	123	3.072e-08
GO:BP	GO:0031570	DNA integrity checkpoint signaling	79	123	3.072e-08
GO:BP	GO:1903432	regulation of TORC1 signaling	65	96	3.698e-08
GO:BP	GO:0007051	spindle organization	119	206	4.168e-08
GO:BP	GO:0031346	positive regulation of cell projection organization	188	357	4.233e-08
GO:BP	GO:0006289	nucleotide-excision repair	58	83	4.408e-08
GO:BP	GO:0031667	response to nutrient levels	255	510	4.633e-08
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	89	144	4.932e-08
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	73	112	4.932e-08
GO:BP	GO:0072659	protein localization to plasma membrane	158	291	5.134e-08
GO:BP	GO:0007052	mitotic spindle organization	84	134	5.210e-08
GO:BP	GO:1902117	positive regulation of organelle assembly	61	89	5.545e-08
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	1322	3157	5.553e-08
GO:BP	GO:0034504	protein localization to nucleus	170	318	5.887e-08
GO:BP	GO:0007417	central nervous system development	486	1061	6.187e-08
GO:BP	GO:0022604	regulation of cell morphogenesis	137	246	6.862e-08
GO:BP	GO:1901873	regulation of post-translational protein modification	136	244	7.269e-08
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	147	268	7.367e-08
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	141	255	7.598e-08
GO:BP	GO:0044088	regulation of vacuole organization	45	60	8.069e-08
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	197	380	8.845e-08
GO:BP	GO:0050767	regulation of neurogenesis	196	378	9.483e-08
GO:BP	GO:0051648	vesicle localization	124	219	9.931e-08
GO:BP	GO:0016239	positive regulation of macroautophagy	60	88	1.003e-07
GO:BP	GO:0051650	establishment of vesicle localization	115	200	1.081e-07
GO:BP	GO:0030162	regulation of proteolysis	208	406	1.151e-07
GO:BP	GO:0001558	regulation of cell growth	208	406	1.151e-07
GO:BP	GO:0007032	endosome organization	65	98	1.274e-07
GO:BP	GO:0031109	microtubule polymerization or depolymerization	85	138	1.375e-07
GO:BP	GO:0051983	regulation of chromosome segregation	82	132	1.441e-07
GO:BP	GO:0099003	vesicle-mediated transport in synapse	141	257	1.471e-07
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	75	118	1.498e-07
GO:BP	GO:0006275	regulation of DNA replication	76	120	1.498e-07
GO:BP	GO:0032940	secretion by cell	398	854	1.517e-07
GO:BP	GO:1901700	response to oxygen-containing compound	730	1669	1.519e-07
GO:BP	GO:0009303	rRNA transcription	33	40	1.519e-07
GO:BP	GO:0098727	maintenance of cell number	107	184	1.552e-07
GO:BP	GO:0016358	dendrite development	134	242	1.588e-07
GO:BP	GO:0062197	cellular response to chemical stress	168	317	1.588e-07
GO:BP	GO:0019827	stem cell population maintenance	105	180	1.689e-07
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	50	70	1.692e-07
GO:BP	GO:0007034	vacuolar transport	102	174	1.921e-07
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	62	93	2.063e-07
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	52	74	2.096e-07
GO:BP	GO:0016482	cytosolic transport	86	141	2.121e-07
GO:BP	GO:0060322	head development	377	806	2.251e-07
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	115	202	2.251e-07
GO:BP	GO:0051960	regulation of nervous system development	229	457	2.251e-07
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	67	103	2.360e-07
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	68	105	2.397e-07
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	69	107	2.425e-07
GO:BP	GO:0035967	cellular response to topologically incorrect protein	70	109	2.446e-07
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	132	239	2.467e-07
GO:BP	GO:0010821	regulation of mitochondrion organization	73	115	2.470e-07
GO:BP	GO:0021915	neural tube development	95	160	2.480e-07
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	165	312	2.541e-07
GO:BP	GO:2000785	regulation of autophagosome assembly	38	49	2.615e-07
GO:BP	GO:0050821	protein stabilization	125	224	2.625e-07
GO:BP	GO:0140352	export from cell	427	928	2.815e-07
GO:BP	GO:0099173	postsynapse organization	135	246	2.837e-07
GO:BP	GO:0032886	regulation of microtubule-based process	144	266	3.060e-07
GO:BP	GO:0006887	exocytosis	186	360	3.081e-07
GO:BP	GO:0032006	regulation of TOR signaling	88	146	3.102e-07
GO:BP	GO:0009150	purine ribonucleotide metabolic process	182	351	3.114e-07
GO:BP	GO:0005975	carbohydrate metabolic process	273	561	3.119e-07
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	166	315	3.119e-07
GO:BP	GO:0006986	response to unfolded protein	85	140	3.354e-07
GO:BP	GO:0072175	epithelial tube formation	83	136	3.522e-07
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	63	96	3.756e-07
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	66	102	3.987e-07
GO:BP	GO:0006626	protein targeting to mitochondrion	67	104	4.031e-07
GO:BP	GO:0007163	establishment or maintenance of cell polarity	129	234	4.039e-07
GO:BP	GO:0042149	cellular response to glucose starvation	36	46	4.055e-07
GO:BP	GO:0003279	cardiac septum development	69	108	4.072e-07
GO:BP	GO:1901701	cellular response to oxygen-containing compound	530	1182	4.084e-07
GO:BP	GO:0048863	stem cell differentiation	134	245	4.099e-07
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	92	155	4.132e-07
GO:BP	GO:0007030	Golgi organization	91	153	4.282e-07
GO:BP	GO:0009314	response to radiation	219	437	4.394e-07
GO:BP	GO:0035051	cardiocyte differentiation	90	151	4.423e-07
GO:BP	GO:0043254	regulation of protein-containing complex assembly	212	421	4.506e-07
GO:BP	GO:0050808	synapse organization	273	563	4.591e-07
GO:BP	GO:0048762	mesenchymal cell differentiation	137	252	4.634e-07
GO:BP	GO:0006997	nucleus organization	88	147	4.706e-07
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	41	55	4.841e-07
GO:BP	GO:0048598	embryonic morphogenesis	297	620	4.940e-07
GO:BP	GO:0006479	protein methylation	37	48	5.148e-07
GO:BP	GO:0008213	protein alkylation	37	48	5.148e-07
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	501	1113	5.402e-07
GO:BP	GO:0060606	tube closure	59	89	5.889e-07
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	79	129	5.990e-07
GO:BP	GO:0032869	cellular response to insulin stimulus	116	207	5.990e-07
GO:BP	GO:0006405	RNA export from nucleus	60	91	6.050e-07
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	49	70	6.237e-07
GO:BP	GO:0007265	Ras protein signal transduction	76	123	6.319e-07
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	63	97	6.461e-07
GO:BP	GO:0055007	cardiac muscle cell differentiation	73	117	6.569e-07
GO:BP	GO:0060996	dendritic spine development	65	101	6.619e-07
GO:BP	GO:0033045	regulation of sister chromatid segregation	68	107	6.719e-07
GO:BP	GO:0003205	cardiac chamber development	98	169	7.139e-07
GO:BP	GO:0035148	tube formation	88	148	7.139e-07
GO:BP	GO:0031401	positive regulation of protein modification process	303	637	8.193e-07
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	82	136	8.728e-07
GO:BP	GO:0044843	cell cycle G1/S phase transition	126	230	9.065e-07
GO:BP	GO:0032970	regulation of actin filament-based process	191	376	9.474e-07
GO:BP	GO:0048871	multicellular organismal-level homeostasis	381	825	9.834e-07
GO:BP	GO:0001843	neural tube closure	58	88	1.026e-06
GO:BP	GO:0014020	primary neural tube formation	61	94	1.095e-06
GO:BP	GO:0034620	cellular response to unfolded protein	61	94	1.095e-06
GO:BP	GO:1990928	response to amino acid starvation	41	56	1.100e-06
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	63	98	1.120e-06
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	64	100	1.127e-06
GO:BP	GO:0001568	blood vessel development	342	732	1.129e-06
GO:BP	GO:0051310	metaphase chromosome alignment	66	104	1.129e-06
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	166	320	1.169e-06
GO:BP	GO:0048589	developmental growth	313	663	1.203e-06
GO:BP	GO:2000779	regulation of double-strand break repair	85	143	1.209e-06
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	49	71	1.227e-06
GO:BP	GO:0046488	phosphatidylinositol metabolic process	94	162	1.257e-06
GO:BP	GO:0050803	regulation of synapse structure or activity	164	316	1.336e-06
GO:BP	GO:0034329	cell junction assembly	245	503	1.412e-06
GO:BP	GO:0060395	SMAD protein signal transduction	54	81	1.621e-06
GO:BP	GO:0006352	DNA-templated transcription initiation	116	210	1.641e-06
GO:BP	GO:0001838	embryonic epithelial tube formation	75	123	1.641e-06
GO:BP	GO:0007088	regulation of mitotic nuclear division	74	121	1.675e-06
GO:BP	GO:0099504	synaptic vesicle cycle	121	221	1.678e-06
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	115	208	1.736e-06
GO:BP	GO:0007420	brain development	350	754	1.768e-06
GO:BP	GO:0006457	protein folding	120	219	1.779e-06
GO:BP	GO:1901800	positive regulation of proteasomal protein catabolic process	70	113	1.796e-06
GO:BP	GO:0034198	cellular response to amino acid starvation	39	53	1.798e-06
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	85	144	1.827e-06
GO:BP	GO:0001841	neural tube formation	64	101	1.881e-06
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	63	99	1.881e-06
GO:BP	GO:0001944	vasculature development	353	762	1.987e-06
GO:BP	GO:0030010	establishment of cell polarity	92	159	2.019e-06
GO:BP	GO:0032007	negative regulation of TOR signaling	47	68	2.062e-06
GO:BP	GO:0060485	mesenchyme development	165	320	2.075e-06
GO:BP	GO:0060284	regulation of cell development	388	847	2.089e-06
GO:BP	GO:0046434	organophosphate catabolic process	132	246	2.094e-06
GO:BP	GO:0009411	response to UV	90	155	2.202e-06
GO:BP	GO:0032870	cellular response to hormone stimulus	301	638	2.230e-06
GO:BP	GO:0050807	regulation of synapse organization	160	309	2.248e-06
GO:BP	GO:1901292	nucleoside phosphate catabolic process	104	185	2.273e-06
GO:BP	GO:0043434	response to peptide hormone	217	440	2.275e-06
GO:BP	GO:0003015	heart process	135	253	2.301e-06
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	139	262	2.361e-06
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	297	629	2.436e-06
GO:BP	GO:0050000	chromosome localization	76	126	2.447e-06
GO:BP	GO:0044282	small molecule catabolic process	187	371	2.469e-06
GO:BP	GO:0060173	limb development	108	194	2.544e-06
GO:BP	GO:0048736	appendage development	108	194	2.544e-06
GO:BP	GO:0071559	response to transforming growth factor beta	142	269	2.552e-06
GO:BP	GO:0006082	organic acid metabolic process	415	915	2.904e-06
GO:BP	GO:0061157	mRNA destabilization	64	102	3.099e-06
GO:BP	GO:0045739	positive regulation of DNA repair	81	137	3.181e-06
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	44	63	3.183e-06
GO:BP	GO:0060429	epithelium development	546	1238	3.200e-06
GO:BP	GO:0060627	regulation of vesicle-mediated transport	255	531	3.306e-06
GO:BP	GO:0030522	intracellular receptor signaling pathway	189	377	3.402e-06
GO:BP	GO:0000959	mitochondrial RNA metabolic process	38	52	3.402e-06
GO:BP	GO:0046903	secretion	446	992	3.409e-06
GO:BP	GO:0051223	regulation of protein transport	217	442	3.436e-06
GO:BP	GO:0043436	oxoacid metabolic process	412	909	3.474e-06
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	88	152	3.500e-06
GO:BP	GO:1904951	positive regulation of establishment of protein localization	168	329	3.509e-06
GO:BP	GO:0007269	neurotransmitter secretion	87	150	3.653e-06
GO:BP	GO:0099643	signal release from synapse	87	150	3.653e-06
GO:BP	GO:0008016	regulation of heart contraction	112	204	3.873e-06
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	47	69	3.896e-06
GO:BP	GO:0043549	regulation of kinase activity	212	431	3.918e-06
GO:BP	GO:1903008	organelle disassembly	48	71	4.111e-06
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	49	73	4.307e-06
GO:BP	GO:0043112	receptor metabolic process	49	73	4.307e-06
GO:BP	GO:0043066	negative regulation of apoptotic process	397	874	4.319e-06
GO:BP	GO:0090068	positive regulation of cell cycle process	138	262	4.355e-06
GO:BP	GO:0032206	positive regulation of telomere maintenance	50	75	4.473e-06
GO:BP	GO:0018205	peptidyl-lysine modification	82	140	4.518e-06
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	41	58	4.827e-06
GO:BP	GO:0019752	carboxylic acid metabolic process	402	887	4.834e-06
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	144	276	5.014e-06
GO:BP	GO:0030488	tRNA methylation	31	40	5.048e-06
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	56	87	5.103e-06
GO:BP	GO:0001503	ossification	211	430	5.141e-06
GO:BP	GO:0051146	striated muscle cell differentiation	155	301	5.153e-06
GO:BP	GO:0034599	cellular response to oxidative stress	131	247	5.195e-06
GO:BP	GO:0099175	regulation of postsynapse organization	87	151	5.312e-06
GO:BP	GO:0036294	cellular response to decreased oxygen levels	86	149	5.574e-06
GO:BP	GO:0009166	nucleotide catabolic process	92	162	6.026e-06
GO:BP	GO:0048813	dendrite morphogenesis	84	145	6.117e-06
GO:BP	GO:0032868	response to insulin	141	270	6.117e-06
GO:BP	GO:0051303	establishment of chromosome localization	71	118	6.744e-06
GO:BP	GO:0001837	epithelial to mesenchymal transition	96	171	6.950e-06
GO:BP	GO:0098657	import into cell	415	922	7.564e-06
GO:BP	GO:0050779	RNA destabilization	65	106	7.899e-06
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	65	106	7.899e-06
GO:BP	GO:0060047	heart contraction	129	244	7.908e-06
GO:BP	GO:0071453	cellular response to oxygen levels	93	165	8.169e-06
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	86	150	8.169e-06
GO:BP	GO:0051098	regulation of binding	115	213	8.169e-06
GO:BP	GO:0033119	negative regulation of RNA splicing	23	27	8.249e-06
GO:BP	GO:0016032	viral process	207	423	8.314e-06
GO:BP	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	52	80	8.364e-06
GO:BP	GO:0031123	RNA 3’-end processing	60	96	8.478e-06
GO:BP	GO:0051304	chromosome separation	54	84	8.540e-06
GO:BP	GO:0061337	cardiac conduction	59	94	8.540e-06
GO:BP	GO:0031124	mRNA 3’-end processing	34	46	9.128e-06
GO:BP	GO:0045862	positive regulation of proteolysis	117	218	9.639e-06
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	41	59	9.639e-06
GO:BP	GO:0051147	regulation of muscle cell differentiation	82	142	9.814e-06
GO:BP	GO:0060048	cardiac muscle contraction	82	142	9.814e-06
GO:BP	GO:0030097	hemopoiesis	436	976	1.036e-05
GO:BP	GO:0051898	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	42	61	1.036e-05
GO:BP	GO:0035107	appendage morphogenesis	88	155	1.054e-05
GO:BP	GO:0035108	limb morphogenesis	88	155	1.054e-05
GO:BP	GO:0072523	purine-containing compound catabolic process	88	155	1.054e-05
GO:BP	GO:0043069	negative regulation of programmed cell death	407	905	1.056e-05
GO:BP	GO:0001501	skeletal system development	256	540	1.079e-05
GO:BP	GO:0097352	autophagosome maturation	43	63	1.094e-05
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	43	63	1.094e-05
GO:BP	GO:0051093	negative regulation of developmental process	415	925	1.108e-05
GO:BP	GO:0051306	mitotic sister chromatid separation	44	65	1.157e-05
GO:BP	GO:0035265	organ growth	92	164	1.208e-05
GO:BP	GO:0051783	regulation of nuclear division	85	149	1.225e-05
GO:BP	GO:0000422	autophagy of mitochondrion	64	105	1.257e-05
GO:BP	GO:0060411	cardiac septum morphogenesis	46	69	1.261e-05
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	47	71	1.305e-05
GO:BP	GO:0009887	animal organ morphogenesis	462	1042	1.311e-05
GO:BP	GO:0031396	regulation of protein ubiquitination	107	197	1.323e-05
GO:BP	GO:0046395	carboxylic acid catabolic process	129	246	1.344e-05
GO:BP	GO:0016054	organic acid catabolic process	129	246	1.344e-05
GO:BP	GO:0045787	positive regulation of cell cycle	175	351	1.360e-05
GO:BP	GO:0009725	response to hormone	407	907	1.367e-05
GO:BP	GO:1905818	regulation of chromosome separation	50	77	1.387e-05
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	51	79	1.405e-05
GO:BP	GO:0006979	response to oxidative stress	196	400	1.415e-05
GO:BP	GO:0048514	blood vessel morphogenesis	295	635	1.415e-05
GO:BP	GO:0035050	embryonic heart tube development	55	87	1.419e-05
GO:BP	GO:0071478	cellular response to radiation	100	182	1.466e-05
GO:BP	GO:0060999	positive regulation of dendritic spine development	32	43	1.469e-05
GO:BP	GO:0051053	negative regulation of DNA metabolic process	80	139	1.549e-05
GO:BP	GO:0006301	postreplication repair	28	36	1.572e-05
GO:BP	GO:0061001	regulation of dendritic spine morphogenesis	33	45	1.730e-05
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	97	176	1.760e-05
GO:BP	GO:0007004	telomere maintenance via telomerase	41	60	1.839e-05
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	154	304	1.839e-05
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	154	304	1.839e-05
GO:BP	GO:0003231	cardiac ventricle development	74	127	2.052e-05
GO:BP	GO:0045859	regulation of protein kinase activity	196	402	2.136e-05
GO:BP	GO:0000910	cytokinesis	104	192	2.166e-05
GO:BP	GO:0031032	actomyosin structure organization	113	212	2.208e-05
GO:BP	GO:0051050	positive regulation of transport	381	847	2.251e-05
GO:BP	GO:0006406	mRNA export from nucleus	46	70	2.257e-05
GO:BP	GO:0046777	protein autophosphorylation	98	179	2.289e-05
GO:BP	GO:2000278	regulation of DNA biosynthetic process	57	92	2.290e-05
GO:BP	GO:0042127	regulation of cell population proliferation	717	1685	2.290e-05
GO:BP	GO:0071479	cellular response to ionizing radiation	47	72	2.295e-05
GO:BP	GO:0003013	circulatory system process	280	602	2.311e-05
GO:BP	GO:0031023	microtubule organizing center organization	86	153	2.346e-05
GO:BP	GO:0051865	protein autoubiquitination	49	76	2.355e-05
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	54	86	2.357e-05
GO:BP	GO:0006091	generation of precursor metabolites and energy	228	478	2.367e-05
GO:BP	GO:0007219	Notch signaling pathway	101	186	2.591e-05
GO:BP	GO:0001667	ameboidal-type cell migration	123	235	2.608e-05
GO:BP	GO:0042326	negative regulation of phosphorylation	134	260	2.713e-05
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	134	260	2.713e-05
GO:BP	GO:0017148	negative regulation of translation	76	132	2.726e-05
GO:BP	GO:0007000	nucleolus organization	16	17	2.794e-05
GO:BP	GO:0040029	epigenetic regulation of gene expression	151	299	2.846e-05
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	38	55	2.886e-05
GO:BP	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	38	55	2.886e-05
GO:BP	GO:0046902	regulation of mitochondrial membrane permeability	38	55	2.886e-05
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	64	107	2.984e-05
GO:BP	GO:0009062	fatty acid catabolic process	64	107	2.984e-05
GO:BP	GO:0043087	regulation of GTPase activity	108	202	3.005e-05
GO:BP	GO:0019216	regulation of lipid metabolic process	160	320	3.019e-05
GO:BP	GO:0016180	snRNA processing	27	35	3.146e-05
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	40	59	3.255e-05
GO:BP	GO:0060236	regulation of mitotic spindle organization	32	44	3.258e-05
GO:BP	GO:0003206	cardiac chamber morphogenesis	72	124	3.258e-05
GO:BP	GO:0010628	positive regulation of gene expression	527	1212	3.509e-05
GO:BP	GO:0001649	osteoblast differentiation	122	234	3.625e-05
GO:BP	GO:0051784	negative regulation of nuclear division	43	65	3.670e-05
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	84	150	3.676e-05
GO:BP	GO:1902369	negative regulation of RNA catabolic process	56	91	3.695e-05
GO:BP	GO:0035023	regulation of Rho protein signal transduction	55	89	3.757e-05
GO:BP	GO:0072665	protein localization to vacuole	55	89	3.757e-05
GO:BP	GO:0016477	cell migration	655	1534	3.809e-05
GO:BP	GO:0006643	membrane lipid metabolic process	113	214	3.809e-05
GO:BP	GO:0099536	synaptic signaling	363	807	3.809e-05
GO:BP	GO:0045444	fat cell differentiation	125	241	3.814e-05
GO:BP	GO:2001234	negative regulation of apoptotic signaling pathway	121	232	3.837e-05
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	68	116	3.844e-05
GO:BP	GO:0003143	embryonic heart tube morphogenesis	47	73	3.905e-05
GO:BP	GO:0086001	cardiac muscle cell action potential	51	81	3.910e-05
GO:BP	GO:1904262	negative regulation of TORC1 signaling	34	48	4.069e-05
GO:BP	GO:0099537	trans-synaptic signaling	352	781	4.303e-05
GO:BP	GO:0031577	spindle checkpoint signaling	35	50	4.467e-05
GO:BP	GO:0071985	multivesicular body sorting pathway	35	50	4.467e-05
GO:BP	GO:0032205	negative regulation of telomere maintenance	29	39	4.624e-05
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	133	260	4.718e-05
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	96	177	4.723e-05
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	96	177	4.723e-05
GO:BP	GO:0007098	centrosome cycle	79	140	4.781e-05
GO:BP	GO:0042274	ribosomal small subunit biogenesis	62	104	4.829e-05
GO:BP	GO:0006505	GPI anchor metabolic process	25	32	4.921e-05
GO:BP	GO:0180046	GPI anchored protein biosynthesis	25	32	4.921e-05
GO:BP	GO:0006195	purine nucleotide catabolic process	78	138	5.032e-05
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	165	334	5.053e-05
GO:BP	GO:0006390	mitochondrial transcription	19	22	5.085e-05
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	37	54	5.118e-05
GO:BP	GO:1904263	positive regulation of TORC1 signaling	37	54	5.118e-05
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	77	136	5.288e-05
GO:BP	GO:0048872	homeostasis of number of cells	164	332	5.400e-05
GO:BP	GO:0043534	blood vessel endothelial cell migration	69	119	5.412e-05
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	58	96	5.449e-05
GO:BP	GO:0106027	neuron projection organization	57	94	5.607e-05
GO:BP	GO:0045995	regulation of embryonic development	56	92	5.758e-05
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	41	62	6.101e-05
GO:BP	GO:0044380	protein localization to cytoskeleton	41	62	6.101e-05
GO:BP	GO:0032456	endocytic recycling	53	86	6.157e-05
GO:BP	GO:0062125	regulation of mitochondrial gene expression	26	34	6.169e-05
GO:BP	GO:0140058	neuron projection arborization	26	34	6.169e-05
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	42	64	6.216e-05
GO:BP	GO:0110154	RNA decapping	17	19	6.216e-05
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	17	19	6.216e-05
GO:BP	GO:0018022	peptidyl-lysine methylation	17	19	6.216e-05
GO:BP	GO:0072666	establishment of protein localization to vacuole	43	66	6.331e-05
GO:BP	GO:0019080	viral gene expression	64	109	6.689e-05
GO:BP	GO:1901136	carbohydrate derivative catabolic process	131	257	6.803e-05
GO:BP	GO:0051240	positive regulation of multicellular organismal process	705	1667	6.939e-05
GO:BP	GO:0033157	regulation of intracellular protein transport	84	152	7.032e-05
GO:BP	GO:0008286	insulin receptor signaling pathway	71	124	7.142e-05
GO:BP	GO:0018105	peptidyl-serine phosphorylation	94	174	7.157e-05
GO:BP	GO:1990823	response to leukemia inhibitory factor	62	105	7.225e-05
GO:BP	GO:0007041	lysosomal transport	77	137	7.461e-05
GO:BP	GO:0008637	apoptotic mitochondrial changes	61	103	7.505e-05
GO:BP	GO:0071824	protein-DNA complex organization	133	262	7.511e-05
GO:BP	GO:0030900	forebrain development	202	423	7.619e-05
GO:BP	GO:0007015	actin filament organization	218	461	7.619e-05
GO:BP	GO:0048732	gland development	215	454	7.811e-05
GO:BP	GO:0000165	MAPK cascade	335	744	7.825e-05
GO:BP	GO:0071173	spindle assembly checkpoint signaling	34	49	7.980e-05
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	34	49	7.980e-05
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	34	49	7.980e-05
GO:BP	GO:0019725	cellular homeostasis	372	835	8.003e-05
GO:BP	GO:0016079	synaptic vesicle exocytosis	59	99	8.003e-05
GO:BP	GO:0062012	regulation of small molecule metabolic process	158	320	8.007e-05
GO:BP	GO:0010507	negative regulation of autophagy	56	93	8.870e-05
GO:BP	GO:0070482	response to oxygen levels	168	344	9.289e-05
GO:BP	GO:0071456	cellular response to hypoxia	79	142	9.343e-05
GO:BP	GO:0006109	regulation of carbohydrate metabolic process	94	175	9.617e-05
GO:BP	GO:0098916	anterograde trans-synaptic signaling	347	775	9.648e-05
GO:BP	GO:0007268	chemical synaptic transmission	347	775	9.648e-05
GO:BP	GO:0006413	translational initiation	72	127	9.688e-05
GO:BP	GO:0006506	GPI anchor biosynthetic process	24	31	9.759e-05
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	38	57	9.844e-05
GO:BP	GO:1900077	negative regulation of cellular response to insulin stimulus	29	40	9.999e-05
GO:BP	GO:0097061	dendritic spine organization	51	83	1.006e-04
GO:BP	GO:0001933	negative regulation of protein phosphorylation	125	245	1.013e-04
GO:BP	GO:0086003	cardiac muscle cell contraction	50	81	1.024e-04
GO:BP	GO:0003229	ventricular cardiac muscle tissue development	41	63	1.056e-04
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	41	63	1.056e-04
GO:BP	GO:0031397	negative regulation of protein ubiquitination	48	77	1.056e-04
GO:BP	GO:0010586	miRNA metabolic process	62	106	1.066e-04
GO:BP	GO:0006664	glycolipid metabolic process	62	106	1.066e-04
GO:BP	GO:0055117	regulation of cardiac muscle contraction	47	75	1.066e-04
GO:BP	GO:0044283	small molecule biosynthetic process	272	593	1.084e-04
GO:BP	GO:0086012	membrane depolarization during cardiac muscle cell action potential	18	21	1.098e-04
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	61	104	1.110e-04
GO:BP	GO:0048638	regulation of developmental growth	153	310	1.121e-04
GO:BP	GO:0006941	striated muscle contraction	100	189	1.143e-04
GO:BP	GO:1990253	cellular response to leucine starvation	12	12	1.150e-04
GO:BP	GO:0060421	positive regulation of heart growth	25	33	1.194e-04
GO:BP	GO:0043247	telomere maintenance in response to DNA damage	25	33	1.194e-04
GO:BP	GO:0031116	positive regulation of microtubule polymerization	25	33	1.194e-04
GO:BP	GO:0030258	lipid modification	103	196	1.235e-04
GO:BP	GO:0008285	negative regulation of cell population proliferation	318	706	1.250e-04
GO:BP	GO:0061448	connective tissue development	145	292	1.264e-04
GO:BP	GO:0044092	negative regulation of molecular function	255	553	1.275e-04
GO:BP	GO:0009890	negative regulation of biosynthetic process	1149	2813	1.307e-04
GO:BP	GO:0006836	neurotransmitter transport	110	212	1.312e-04
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	128	253	1.315e-04
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	32	46	1.329e-04
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	65	113	1.360e-04
GO:BP	GO:0090224	regulation of spindle organization	33	48	1.426e-04
GO:BP	GO:0006458	‘de novo’ protein folding	33	48	1.426e-04
GO:BP	GO:0072384	organelle transport along microtubule	54	90	1.432e-04
GO:BP	GO:0034502	protein localization to chromosome	71	126	1.432e-04
GO:BP	GO:0034644	cellular response to UV	54	90	1.432e-04
GO:BP	GO:0150104	transport across blood-brain barrier	53	88	1.474e-04
GO:BP	GO:0036293	response to decreased oxygen levels	155	316	1.474e-04
GO:BP	GO:0010232	vascular transport	53	88	1.474e-04
GO:BP	GO:1901836	regulation of transcription of nucleolar large rRNA by RNA polymerase I	14	15	1.512e-04
GO:BP	GO:1903509	liposaccharide metabolic process	62	107	1.562e-04
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	154	314	1.577e-04
GO:BP	GO:0043547	positive regulation of GTPase activity	75	135	1.610e-04
GO:BP	GO:2000736	regulation of stem cell differentiation	49	80	1.637e-04
GO:BP	GO:0006414	translational elongation	49	80	1.637e-04
GO:BP	GO:0010761	fibroblast migration	36	54	1.637e-04
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	27	37	1.637e-04
GO:BP	GO:0051258	protein polymerization	141	284	1.648e-04
GO:BP	GO:0048754	branching morphogenesis of an epithelial tube	85	157	1.655e-04
GO:BP	GO:0043489	RNA stabilization	48	78	1.669e-04
GO:BP	GO:0050686	negative regulation of mRNA processing	19	23	1.673e-04
GO:BP	GO:0150115	cell-substrate junction organization	60	103	1.689e-04
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	98	186	1.689e-04
GO:BP	GO:0018209	peptidyl-serine modification	98	186	1.689e-04
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	74	133	1.689e-04
GO:BP	GO:1990830	cellular response to leukemia inhibitory factor	60	103	1.689e-04
GO:BP	GO:0035329	hippo signaling	38	58	1.709e-04
GO:BP	GO:0032786	positive regulation of DNA-templated transcription, elongation	38	58	1.709e-04
GO:BP	GO:0060997	dendritic spine morphogenesis	39	60	1.738e-04
GO:BP	GO:0051494	negative regulation of cytoskeleton organization	84	155	1.746e-04
GO:BP	GO:0002027	regulation of heart rate	59	101	1.758e-04
GO:BP	GO:1905515	non-motile cilium assembly	43	68	1.760e-04
GO:BP	GO:0009100	glycoprotein metabolic process	178	371	1.760e-04
GO:BP	GO:0031122	cytoplasmic microtubule organization	42	66	1.763e-04
GO:BP	GO:0007416	synapse assembly	130	259	1.779e-04
GO:BP	GO:0031345	negative regulation of cell projection organization	97	184	1.791e-04
GO:BP	GO:0046627	negative regulation of insulin receptor signaling pathway	28	39	1.820e-04
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	78	142	1.834e-04
GO:BP	GO:0005996	monosaccharide metabolic process	126	250	1.860e-04
GO:BP	GO:0065004	protein-DNA complex assembly	122	241	1.943e-04
GO:BP	GO:0032509	endosome transport via multivesicular body sorting pathway	29	41	2.020e-04
GO:BP	GO:0032790	ribosome disassembly	29	41	2.020e-04
GO:BP	GO:0061138	morphogenesis of a branching epithelium	99	189	2.062e-04
GO:BP	GO:0019395	fatty acid oxidation	63	110	2.134e-04
GO:BP	GO:0072524	pyridine-containing compound metabolic process	90	169	2.143e-04
GO:BP	GO:0007517	muscle organ development	175	365	2.151e-04
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	117	230	2.157e-04
GO:BP	GO:0051225	spindle assembly	75	136	2.192e-04
GO:BP	GO:0009261	ribonucleotide catabolic process	75	136	2.192e-04
GO:BP	GO:0035418	protein localization to synapse	53	89	2.215e-04
GO:BP	GO:0043543	protein acylation	53	89	2.215e-04
GO:BP	GO:0043542	endothelial cell migration	113	221	2.217e-04
GO:BP	GO:0060674	placenta blood vessel development	24	32	2.278e-04
GO:BP	GO:0009301	snRNA transcription	17	20	2.339e-04
GO:BP	GO:0007007	inner mitochondrial membrane organization	31	45	2.350e-04
GO:BP	GO:0090148	membrane fission	31	45	2.350e-04
GO:BP	GO:1901875	positive regulation of post-translational protein modification	73	132	2.464e-04
GO:BP	GO:1902414	protein localization to cell junction	67	119	2.466e-04
GO:BP	GO:0048608	reproductive structure development	153	314	2.473e-04
GO:BP	GO:0030308	negative regulation of cell growth	92	174	2.477e-04
GO:BP	GO:0009101	glycoprotein biosynthetic process	147	300	2.481e-04
GO:BP	GO:0006984	ER-nucleus signaling pathway	32	47	2.481e-04
GO:BP	GO:0051294	establishment of spindle orientation	32	47	2.481e-04
GO:BP	GO:1901888	regulation of cell junction assembly	131	263	2.576e-04
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	48	79	2.580e-04
GO:BP	GO:0042073	intraciliary transport	33	49	2.602e-04
GO:BP	GO:0009247	glycolipid biosynthetic process	47	77	2.646e-04
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	34	51	2.694e-04
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	34	51	2.694e-04
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	34	51	2.694e-04
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	34	51	2.694e-04
GO:BP	GO:0003281	ventricular septum development	45	73	2.756e-04
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	45	73	2.756e-04
GO:BP	GO:0051985	negative regulation of chromosome segregation	35	53	2.759e-04
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	35	53	2.759e-04
GO:BP	GO:0030490	maturation of SSU-rRNA	35	53	2.759e-04
GO:BP	GO:0051345	positive regulation of hydrolase activity	106	206	2.759e-04
GO:BP	GO:1905819	negative regulation of chromosome separation	35	53	2.759e-04
GO:BP	GO:0046785	microtubule polymerization	57	98	2.778e-04
GO:BP	GO:0140374	antiviral innate immune response	36	55	2.816e-04
GO:BP	GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process	36	55	2.816e-04
GO:BP	GO:0002028	regulation of sodium ion transport	43	69	2.820e-04
GO:BP	GO:0048255	mRNA stabilization	43	69	2.820e-04
GO:BP	GO:0090559	regulation of membrane permeability	43	69	2.820e-04
GO:BP	GO:0001947	heart looping	42	67	2.853e-04
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	70	126	2.872e-04
GO:BP	GO:0048814	regulation of dendrite morphogenesis	41	65	2.873e-04
GO:BP	GO:0060998	regulation of dendritic spine development	39	61	2.884e-04
GO:BP	GO:0001822	kidney development	156	322	2.927e-04
GO:BP	GO:0001525	angiogenesis	250	547	3.020e-04
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	69	124	3.034e-04
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	69	124	3.034e-04
GO:BP	GO:1902904	negative regulation of supramolecular fiber organization	84	157	3.072e-04
GO:BP	GO:0006606	protein import into nucleus	88	166	3.156e-04
GO:BP	GO:0051259	protein complex oligomerization	134	271	3.169e-04
GO:BP	GO:0072001	renal system development	160	332	3.272e-04
GO:BP	GO:0048568	embryonic organ development	215	463	3.272e-04
GO:BP	GO:0007409	axonogenesis	215	463	3.272e-04
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	27	38	3.299e-04
GO:BP	GO:1905508	protein localization to microtubule organizing center	27	38	3.299e-04
GO:BP	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	27	38	3.299e-04
GO:BP	GO:0006897	endocytosis	316	709	3.311e-04
GO:BP	GO:0061458	reproductive system development	154	318	3.332e-04
GO:BP	GO:0032042	mitochondrial DNA metabolic process	18	22	3.394e-04
GO:BP	GO:0048025	negative regulation of mRNA splicing, via spliceosome	18	22	3.394e-04
GO:BP	GO:1903322	positive regulation of protein modification by small protein conjugation or removal	72	131	3.514e-04
GO:BP	GO:0019362	pyridine nucleotide metabolic process	86	162	3.576e-04
GO:BP	GO:0046496	nicotinamide nucleotide metabolic process	86	162	3.576e-04
GO:BP	GO:0030334	regulation of cell migration	417	960	3.593e-04
GO:BP	GO:0060412	ventricular septum morphogenesis	28	40	3.593e-04
GO:BP	GO:0055023	positive regulation of cardiac muscle tissue growth	22	29	3.603e-04
GO:BP	GO:0001666	response to hypoxia	147	302	3.603e-04
GO:BP	GO:0086010	membrane depolarization during action potential	22	29	3.603e-04
GO:BP	GO:0051170	import into nucleus	90	171	3.609e-04
GO:BP	GO:0009154	purine ribonucleotide catabolic process	71	129	3.710e-04
GO:BP	GO:0032388	positive regulation of intracellular transport	76	140	3.743e-04
GO:BP	GO:0045022	early endosome to late endosome transport	29	42	3.856e-04
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	1116	2745	3.875e-04
GO:BP	GO:1904375	regulation of protein localization to cell periphery	80	149	3.930e-04
GO:BP	GO:0045727	positive regulation of translation	75	138	3.984e-04
GO:BP	GO:0010976	positive regulation of neuron projection development	84	158	4.055e-04
GO:BP	GO:1903522	regulation of blood circulation	127	256	4.091e-04
GO:BP	GO:0048511	rhythmic process	148	305	4.093e-04
GO:BP	GO:0006635	fatty acid beta-oxidation	46	76	4.125e-04
GO:BP	GO:0090307	mitotic spindle assembly	46	76	4.125e-04
GO:BP	GO:0006942	regulation of striated muscle contraction	56	97	4.182e-04
GO:BP	GO:0030218	erythrocyte differentiation	74	136	4.225e-04
GO:BP	GO:0003254	regulation of membrane depolarization	31	46	4.274e-04
GO:BP	GO:0071773	cellular response to BMP stimulus	87	165	4.389e-04
GO:BP	GO:0071772	response to BMP	87	165	4.389e-04
GO:BP	GO:2000145	regulation of cell motility	441	1022	4.408e-04
GO:BP	GO:0006623	protein targeting to vacuole	32	48	4.426e-04
GO:BP	GO:0071763	nuclear membrane organization	32	48	4.426e-04
GO:BP	GO:0003208	cardiac ventricle morphogenesis	43	70	4.430e-04
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	78	145	4.430e-04
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	155	322	4.507e-04
GO:BP	GO:0035567	non-canonical Wnt signaling pathway	42	68	4.519e-04
GO:BP	GO:0042790	nucleolar large rRNA transcription by RNA polymerase I	19	24	4.547e-04
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	19	24	4.547e-04
GO:BP	GO:0030509	BMP signaling pathway	82	154	4.568e-04
GO:BP	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	41	66	4.584e-04
GO:BP	GO:0009299	mRNA transcription	34	52	4.623e-04
GO:BP	GO:0002262	myeloid cell homeostasis	94	181	4.653e-04
GO:BP	GO:0001763	morphogenesis of a branching structure	105	206	4.663e-04
GO:BP	GO:0098732	macromolecule deacylation	37	58	4.732e-04
GO:BP	GO:1904505	regulation of telomere maintenance in response to DNA damage	16	19	4.854e-04
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	60	106	4.880e-04
GO:BP	GO:0051961	negative regulation of nervous system development	76	141	5.006e-04
GO:BP	GO:0046467	membrane lipid biosynthetic process	80	150	5.202e-04
GO:BP	GO:0030879	mammary gland development	75	139	5.348e-04
GO:BP	GO:0050775	positive regulation of dendrite morphogenesis	25	35	5.467e-04
GO:BP	GO:0060419	heart growth	49	83	5.649e-04
GO:BP	GO:0006446	regulation of translational initiation	49	83	5.649e-04
GO:BP	GO:0030326	embryonic limb morphogenesis	69	126	5.694e-04
GO:BP	GO:0072329	monocarboxylic acid catabolic process	69	126	5.694e-04
GO:BP	GO:0035113	embryonic appendage morphogenesis	69	126	5.694e-04
GO:BP	GO:0050773	regulation of dendrite development	57	100	5.717e-04
GO:BP	GO:0019985	translesion synthesis	20	26	5.756e-04
GO:BP	GO:0070129	regulation of mitochondrial translation	20	26	5.756e-04
GO:BP	GO:2000178	negative regulation of neural precursor cell proliferation	20	26	5.756e-04
GO:BP	GO:0071539	protein localization to centrosome	26	37	5.972e-04
GO:BP	GO:0000132	establishment of mitotic spindle orientation	26	37	5.972e-04
GO:BP	GO:0043603	amide metabolic process	210	455	5.990e-04
GO:BP	GO:1990542	mitochondrial transmembrane transport	56	98	5.995e-04
GO:BP	GO:0002200	somatic diversification of immune receptors	47	79	6.056e-04
GO:BP	GO:0003018	vascular process in circulatory system	133	272	6.163e-04
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	89	171	6.516e-04
GO:BP	GO:0110156	mRNA methylguanosine-cap decapping	14	16	6.599e-04
GO:BP	GO:0045927	positive regulation of growth	126	256	6.607e-04
GO:BP	GO:1901874	negative regulation of post-translational protein modification	54	94	6.633e-04
GO:BP	GO:1901838	positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	10	10	6.746e-04
GO:BP	GO:1990700	nucleolar chromatin organization	10	10	6.746e-04
GO:BP	GO:0045667	regulation of osteoblast differentiation	71	131	6.842e-04
GO:BP	GO:0007224	smoothened signaling pathway	80	151	6.878e-04
GO:BP	GO:0010594	regulation of endothelial cell migration	88	169	6.947e-04
GO:BP	GO:0051383	kinetochore organization	17	21	6.978e-04
GO:BP	GO:2000144	positive regulation of DNA-templated transcription initiation	42	69	7.104e-04
GO:BP	GO:0045596	negative regulation of cell differentiation	298	671	7.105e-04
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	29	43	7.147e-04
GO:BP	GO:0034248	regulation of amide metabolic process	41	67	7.278e-04
GO:BP	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	59	105	7.280e-04
GO:BP	GO:0046622	positive regulation of organ growth	30	45	7.407e-04
GO:BP	GO:1903573	negative regulation of response to endoplasmic reticulum stress	30	45	7.407e-04
GO:BP	GO:0008406	gonad development	118	238	7.441e-04
GO:BP	GO:0070085	glycosylation	121	245	7.494e-04
GO:BP	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	31	47	7.599e-04
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	31	47	7.599e-04
GO:BP	GO:0070914	UV-damage excision repair	12	13	7.787e-04
GO:BP	GO:0006998	nuclear envelope organization	37	59	7.787e-04
GO:BP	GO:0034101	erythrocyte homeostasis	78	147	7.787e-04
GO:BP	GO:1902902	negative regulation of autophagosome assembly	12	13	7.787e-04
GO:BP	GO:0051058	negative regulation of small GTPase mediated signal transduction	36	57	7.811e-04
GO:BP	GO:0046578	regulation of Ras protein signal transduction	33	51	7.811e-04
GO:BP	GO:0032507	maintenance of protein location in cell	36	57	7.811e-04
GO:BP	GO:0048878	chemical homeostasis	447	1043	7.811e-04
GO:BP	GO:0031297	replication fork processing	33	51	7.811e-04
GO:BP	GO:0046034	ATP metabolic process	114	229	7.812e-04
GO:BP	GO:0048284	organelle fusion	86	165	7.841e-04
GO:BP	GO:0022406	membrane docking	50	86	7.893e-04
GO:BP	GO:0045137	development of primary sexual characteristics	120	243	7.945e-04
GO:BP	GO:0010765	positive regulation of sodium ion transport	22	30	7.972e-04
GO:BP	GO:0006520	amino acid metabolic process	143	297	8.193e-04
GO:BP	GO:0048870	cell motility	742	1793	8.354e-04
GO:BP	GO:0003012	muscle system process	202	438	8.388e-04
GO:BP	GO:0060491	regulation of cell projection assembly	103	204	8.444e-04
GO:BP	GO:0070936	protein K48-linked ubiquitination	56	99	8.461e-04
GO:BP	GO:0050768	negative regulation of neurogenesis	72	134	8.528e-04
GO:BP	GO:0042327	positive regulation of phosphorylation	230	506	8.557e-04
GO:BP	GO:2000142	regulation of DNA-templated transcription initiation	48	82	8.595e-04
GO:BP	GO:0061564	axon development	239	528	8.647e-04
GO:BP	GO:0046165	alcohol biosynthetic process	76	143	8.781e-04
GO:BP	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	23	32	8.989e-04
GO:BP	GO:0060444	branching involved in mammary gland duct morphogenesis	18	23	9.055e-04
GO:BP	GO:0055082	intracellular chemical homeostasis	321	730	9.063e-04
GO:BP	GO:0010977	negative regulation of neuron projection development	71	132	9.063e-04
GO:BP	GO:0050769	positive regulation of neurogenesis	121	246	9.102e-04
GO:BP	GO:0010720	positive regulation of cell development	210	458	9.218e-04
GO:BP	GO:0000281	mitotic cytokinesis	54	95	9.372e-04
GO:BP	GO:0140056	organelle localization by membrane tethering	45	76	9.717e-04
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	53	93	9.858e-04
GO:BP	GO:0072344	rescue of stalled ribosome	24	34	9.858e-04
GO:BP	GO:2000781	positive regulation of double-strand break repair	53	93	9.858e-04
GO:BP	GO:0043535	regulation of blood vessel endothelial cell migration	53	93	9.858e-04
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	24	34	9.858e-04
GO:BP	GO:0086004	regulation of cardiac muscle cell contraction	24	34	9.858e-04
GO:BP	GO:0060260	regulation of transcription initiation by RNA polymerase II	44	74	1.003e-03
GO:BP	GO:0061077	chaperone-mediated protein folding	44	74	1.003e-03
GO:BP	GO:0071806	protein transmembrane transport	44	74	1.003e-03
GO:BP	GO:0021537	telencephalon development	137	284	1.005e-03
GO:BP	GO:0045926	negative regulation of growth	113	228	1.028e-03
GO:BP	GO:0042177	negative regulation of protein catabolic process	64	117	1.029e-03
GO:BP	GO:0110053	regulation of actin filament organization	128	263	1.032e-03
GO:BP	GO:0051150	regulation of smooth muscle cell differentiation	25	36	1.063e-03
GO:BP	GO:0016242	negative regulation of macroautophagy	25	36	1.063e-03
GO:BP	GO:0060045	positive regulation of cardiac muscle cell proliferation	19	25	1.116e-03
GO:BP	GO:0007548	sex differentiation	141	294	1.119e-03
GO:BP	GO:0040012	regulation of locomotion	455	1067	1.119e-03
GO:BP	GO:0043010	camera-type eye development	170	363	1.125e-03
GO:BP	GO:0030513	positive regulation of BMP signaling pathway	26	38	1.130e-03
GO:BP	GO:0007266	Rho protein signal transduction	76	144	1.154e-03
GO:BP	GO:0030336	negative regulation of cell migration	140	292	1.198e-03
GO:BP	GO:0045598	regulation of fat cell differentiation	71	133	1.209e-03
GO:BP	GO:0033619	membrane protein proteolysis	38	62	1.209e-03
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	66	122	1.240e-03
GO:BP	GO:0007423	sensory organ development	277	624	1.245e-03
GO:BP	GO:0046928	regulation of neurotransmitter secretion	48	83	1.258e-03
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	48	83	1.258e-03
GO:BP	GO:0008088	axo-dendritic transport	48	83	1.258e-03
GO:BP	GO:1902108	regulation of mitochondrial membrane permeability involved in apoptotic process	29	44	1.261e-03
GO:BP	GO:1901799	negative regulation of proteasomal protein catabolic process	35	56	1.275e-03
GO:BP	GO:0086065	cell communication involved in cardiac conduction	35	56	1.275e-03
GO:BP	GO:0006284	base-excision repair	30	46	1.282e-03
GO:BP	GO:0098927	vesicle-mediated transport between endosomal compartments	31	48	1.291e-03
GO:BP	GO:0001881	receptor recycling	31	48	1.291e-03
GO:BP	GO:0016601	Rac protein signal transduction	31	48	1.291e-03
GO:BP	GO:0006513	protein monoubiquitination	31	48	1.291e-03
GO:BP	GO:0035601	protein deacylation	32	50	1.294e-03
GO:BP	GO:0032968	positive regulation of transcription elongation by RNA polymerase II	32	50	1.294e-03
GO:BP	GO:0099177	regulation of trans-synaptic signaling	232	514	1.297e-03
GO:BP	GO:0036503	ERAD pathway	60	109	1.299e-03
GO:BP	GO:0010906	regulation of glucose metabolic process	54	96	1.316e-03
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	106	213	1.325e-03
GO:BP	GO:0060348	bone development	109	220	1.339e-03
GO:BP	GO:2000786	positive regulation of autophagosome assembly	16	20	1.405e-03
GO:BP	GO:0034614	cellular response to reactive oxygen species	77	147	1.407e-03
GO:BP	GO:0001654	eye development	191	415	1.413e-03
GO:BP	GO:0150011	regulation of neuron projection arborization	13	15	1.417e-03
GO:BP	GO:0003151	outflow tract morphogenesis	45	77	1.431e-03
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	88	172	1.438e-03
GO:BP	GO:0060541	respiratory system development	111	225	1.443e-03
GO:BP	GO:0009135	purine nucleoside diphosphate metabolic process	63	116	1.477e-03
GO:BP	GO:0009179	purine ribonucleoside diphosphate metabolic process	63	116	1.477e-03
GO:BP	GO:0034440	lipid oxidation	63	116	1.477e-03
GO:BP	GO:0007026	negative regulation of microtubule depolymerization	21	29	1.482e-03
GO:BP	GO:0055017	cardiac muscle tissue growth	44	75	1.488e-03
GO:BP	GO:0061512	protein localization to cilium	44	75	1.488e-03
GO:BP	GO:0120032	regulation of plasma membrane bounded cell projection assembly	101	202	1.492e-03
GO:BP	GO:1903321	negative regulation of protein modification by small protein conjugation or removal	51	90	1.544e-03
GO:BP	GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	43	73	1.551e-03
GO:BP	GO:0016444	somatic cell DNA recombination	43	73	1.551e-03
GO:BP	GO:0050804	modulation of chemical synaptic transmission	231	513	1.567e-03
GO:BP	GO:0051347	positive regulation of transferase activity	141	296	1.587e-03
GO:BP	GO:0051402	neuron apoptotic process	141	296	1.587e-03
GO:BP	GO:0003162	atrioventricular node development	9	9	1.621e-03
GO:BP	GO:0000467	exonucleolytic trimming to generate mature 3’-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	9	9	1.621e-03
GO:BP	GO:0000183	rDNA heterochromatin formation	9	9	1.621e-03
GO:BP	GO:0042796	snRNA transcription by RNA polymerase III	9	9	1.621e-03
GO:BP	GO:0006006	glucose metabolic process	93	184	1.631e-03
GO:BP	GO:0019082	viral protein processing	22	31	1.631e-03
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	22	31	1.631e-03
GO:BP	GO:0070536	protein K63-linked deubiquitination	22	31	1.631e-03
GO:BP	GO:0016445	somatic diversification of immunoglobulins	41	69	1.669e-03
GO:BP	GO:0098930	axonal transport	41	69	1.669e-03
GO:BP	GO:0061008	hepaticobiliary system development	78	150	1.695e-03
GO:BP	GO:0055006	cardiac cell development	49	86	1.701e-03
GO:BP	GO:0006900	vesicle budding from membrane	49	86	1.701e-03
GO:BP	GO:0051241	negative regulation of multicellular organismal process	461	1087	1.713e-03
GO:BP	GO:0044057	regulation of system process	247	553	1.724e-03
GO:BP	GO:0051100	negative regulation of binding	55	99	1.724e-03
GO:BP	GO:0006893	Golgi to plasma membrane transport	40	67	1.725e-03
GO:BP	GO:0046890	regulation of lipid biosynthetic process	92	182	1.737e-03
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	65	121	1.737e-03
GO:BP	GO:1904872	regulation of telomerase RNA localization to Cajal body	11	12	1.741e-03
GO:BP	GO:0051657	maintenance of organelle location	11	12	1.741e-03
GO:BP	GO:0060560	developmental growth involved in morphogenesis	117	240	1.742e-03
GO:BP	GO:0006486	protein glycosylation	111	226	1.744e-03
GO:BP	GO:0043413	macromolecule glycosylation	111	226	1.744e-03
GO:BP	GO:0019318	hexose metabolic process	111	226	1.744e-03
GO:BP	GO:0036257	multivesicular body organization	23	33	1.752e-03
GO:BP	GO:0035024	negative regulation of Rho protein signal transduction	17	22	1.755e-03
GO:BP	GO:0061709	reticulophagy	17	22	1.755e-03
GO:BP	GO:0051145	smooth muscle cell differentiation	39	65	1.768e-03
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	48	84	1.768e-03
GO:BP	GO:0046854	phosphatidylinositol phosphate biosynthetic process	39	65	1.768e-03
GO:BP	GO:0045185	maintenance of protein location	39	65	1.768e-03
GO:BP	GO:0060261	positive regulation of transcription initiation by RNA polymerase II	38	63	1.830e-03
GO:BP	GO:0001824	blastocyst development	64	119	1.835e-03
GO:BP	GO:0048639	positive regulation of developmental growth	84	164	1.846e-03
GO:BP	GO:0000460	maturation of 5.8S rRNA	24	35	1.856e-03
GO:BP	GO:0031114	regulation of microtubule depolymerization	24	35	1.856e-03
GO:BP	GO:1900180	regulation of protein localization to nucleus	76	146	1.914e-03
GO:BP	GO:0061351	neural precursor cell proliferation	87	171	1.915e-03
GO:BP	GO:0060612	adipose tissue development	36	59	1.935e-03
GO:BP	GO:0055008	cardiac muscle tissue morphogenesis	36	59	1.935e-03
GO:BP	GO:0010770	positive regulation of cell morphogenesis	25	37	1.943e-03
GO:BP	GO:0022616	DNA strand elongation	25	37	1.943e-03
GO:BP	GO:0045324	late endosome to vacuole transport	25	37	1.943e-03
GO:BP	GO:0097479	synaptic vesicle localization	35	57	1.980e-03
GO:BP	GO:0040013	negative regulation of locomotion	153	326	1.989e-03
GO:BP	GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	26	39	2.014e-03
GO:BP	GO:0000018	regulation of DNA recombination	75	144	2.040e-03
GO:BP	GO:0003203	endocardial cushion morphogenesis	27	41	2.065e-03
GO:BP	GO:0051099	positive regulation of binding	57	104	2.079e-03
GO:BP	GO:0046463	acylglycerol biosynthetic process	32	51	2.079e-03
GO:BP	GO:0046460	neutral lipid biosynthetic process	32	51	2.079e-03
GO:BP	GO:0000302	response to reactive oxygen species	99	199	2.079e-03
GO:BP	GO:0030330	DNA damage response, signal transduction by p53 class mediator	32	51	2.079e-03
GO:BP	GO:0008089	anterograde axonal transport	32	51	2.079e-03
GO:BP	GO:0031573	mitotic intra-S DNA damage checkpoint signaling	14	17	2.079e-03
GO:BP	GO:0072595	maintenance of protein localization in organelle	28	43	2.084e-03
GO:BP	GO:0040001	establishment of mitotic spindle localization	28	43	2.084e-03
GO:BP	GO:0042789	mRNA transcription by RNA polymerase II	30	47	2.099e-03
GO:BP	GO:0035196	miRNA processing	29	45	2.099e-03
GO:BP	GO:1902116	negative regulation of organelle assembly	30	47	2.099e-03
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	29	45	2.099e-03
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	74	142	2.165e-03
GO:BP	GO:0042982	amyloid precursor protein metabolic process	43	74	2.235e-03
GO:BP	GO:1903578	regulation of ATP metabolic process	43	74	2.235e-03
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	88	174	2.241e-03
GO:BP	GO:0046620	regulation of organ growth	50	89	2.241e-03
GO:BP	GO:0045055	regulated exocytosis	113	232	2.244e-03
GO:BP	GO:0051222	positive regulation of protein transport	124	258	2.309e-03
GO:BP	GO:0051588	regulation of neurotransmitter transport	55	100	2.336e-03
GO:BP	GO:0008333	endosome to lysosome transport	42	72	2.336e-03
GO:BP	GO:0030099	myeloid cell differentiation	201	443	2.345e-03
GO:BP	GO:2000146	negative regulation of cell motility	145	308	2.374e-03
GO:BP	GO:0001508	action potential	87	172	2.398e-03
GO:BP	GO:0022038	corpus callosum development	19	26	2.405e-03
GO:BP	GO:0001889	liver development	76	147	2.448e-03
GO:BP	GO:0150063	visual system development	191	419	2.449e-03
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	72	138	2.472e-03
GO:BP	GO:0048041	focal adhesion assembly	48	85	2.499e-03
GO:BP	GO:1905475	regulation of protein localization to membrane	96	193	2.540e-03
GO:BP	GO:0045814	negative regulation of gene expression, epigenetic	99	200	2.565e-03
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	89	177	2.633e-03
GO:BP	GO:0007044	cell-substrate junction assembly	53	96	2.633e-03
GO:BP	GO:0003300	cardiac muscle hypertrophy	47	83	2.639e-03
GO:BP	GO:0032469	endoplasmic reticulum calcium ion homeostasis	20	28	2.688e-03
GO:BP	GO:0055001	muscle cell development	98	198	2.751e-03
GO:BP	GO:0090672	telomerase RNA localization	15	19	2.759e-03
GO:BP	GO:0090671	telomerase RNA localization to Cajal body	15	19	2.759e-03
GO:BP	GO:0033059	cellular pigmentation	38	64	2.759e-03
GO:BP	GO:0060039	pericardium development	15	19	2.759e-03
GO:BP	GO:0090670	RNA localization to Cajal body	15	19	2.759e-03
GO:BP	GO:0031113	regulation of microtubule polymerization	38	64	2.759e-03
GO:BP	GO:0007076	mitotic chromosome condensation	15	19	2.759e-03
GO:BP	GO:0090685	RNA localization to nucleus	15	19	2.759e-03
GO:BP	GO:0007267	cell-cell signaling	559	1342	2.801e-03
GO:BP	GO:0042733	embryonic digit morphogenesis	37	62	2.855e-03
GO:BP	GO:0051984	positive regulation of chromosome segregation	21	30	2.912e-03
GO:BP	GO:1904357	negative regulation of telomere maintenance via telomere lengthening	21	30	2.912e-03
GO:BP	GO:0000002	mitochondrial genome maintenance	21	30	2.912e-03
GO:BP	GO:1901652	response to peptide	409	962	2.925e-03
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	61	114	2.930e-03
GO:BP	GO:0002520	immune system development	100	203	2.940e-03
GO:BP	GO:0032273	positive regulation of protein polymerization	51	92	2.942e-03
GO:BP	GO:0008631	intrinsic apoptotic signaling pathway in response to oxidative stress	36	60	2.947e-03
GO:BP	GO:0034097	response to cytokine	403	947	2.949e-03
GO:BP	GO:0007100	mitotic centrosome separation	12	14	2.979e-03
GO:BP	GO:0140718	facultative heterochromatin formation	12	14	2.979e-03
GO:BP	GO:0030278	regulation of ossification	65	123	2.982e-03
GO:BP	GO:0061614	miRNA transcription	44	77	3.066e-03
GO:BP	GO:0086019	cell-cell signaling involved in cardiac conduction	22	32	3.092e-03
GO:BP	GO:0036258	multivesicular body assembly	22	32	3.092e-03
GO:BP	GO:2000628	regulation of miRNA metabolic process	50	90	3.112e-03
GO:BP	GO:0009408	response to heat	55	101	3.167e-03
GO:BP	GO:0090398	cellular senescence	55	101	3.167e-03
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	72	139	3.177e-03
GO:BP	GO:0051261	protein depolymerization	64	121	3.182e-03
GO:BP	GO:0055002	striated muscle cell development	86	171	3.198e-03
GO:BP	GO:0043954	cellular component maintenance	43	75	3.216e-03
GO:BP	GO:0006654	phosphatidic acid biosynthetic process	23	34	3.230e-03
GO:BP	GO:1902235	regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	23	34	3.230e-03
GO:BP	GO:0060603	mammary gland duct morphogenesis	23	34	3.230e-03
GO:BP	GO:0048880	sensory system development	193	426	3.263e-03
GO:BP	GO:0010332	response to gamma radiation	32	52	3.290e-03
GO:BP	GO:0009615	response to virus	188	414	3.344e-03
GO:BP	GO:0170036	import into the mitochondrion	31	50	3.355e-03
GO:BP	GO:0007019	microtubule depolymerization	31	50	3.355e-03
GO:BP	GO:0032506	cytokinetic process	31	50	3.355e-03
GO:BP	GO:0061371	determination of heart left/right asymmetry	42	73	3.367e-03
GO:BP	GO:0070242	thymocyte apoptotic process	16	21	3.379e-03
GO:BP	GO:0043244	regulation of protein-containing complex disassembly	67	128	3.404e-03
GO:BP	GO:0098534	centriole assembly	30	48	3.406e-03
GO:BP	GO:0010762	regulation of fibroblast migration	25	38	3.408e-03
GO:BP	GO:0086091	regulation of heart rate by cardiac conduction	26	40	3.457e-03
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	144	308	3.466e-03
GO:BP	GO:0000731	DNA synthesis involved in DNA repair	28	44	3.466e-03
GO:BP	GO:0017004	cytochrome complex assembly	27	42	3.466e-03
GO:BP	GO:0035794	positive regulation of mitochondrial membrane permeability	27	42	3.466e-03
GO:BP	GO:0032787	monocarboxylic acid metabolic process	270	616	3.485e-03
GO:BP	GO:0031398	positive regulation of protein ubiquitination	58	108	3.502e-03
GO:BP	GO:0051668	localization within membrane	393	924	3.568e-03
GO:BP	GO:0001934	positive regulation of protein phosphorylation	216	483	3.587e-03
GO:BP	GO:0070534	protein K63-linked ubiquitination	40	69	3.698e-03
GO:BP	GO:0045445	myoblast differentiation	61	115	3.858e-03
GO:BP	GO:0034394	protein localization to cell surface	39	67	3.877e-03
GO:BP	GO:0018195	peptidyl-arginine modification	10	11	3.877e-03
GO:BP	GO:0044091	membrane biogenesis	39	67	3.877e-03
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	247	560	3.892e-03
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	247	560	3.892e-03
GO:BP	GO:0006937	regulation of muscle contraction	83	165	3.896e-03
GO:BP	GO:0016237	microautophagy	17	23	3.943e-03
GO:BP	GO:0060392	negative regulation of SMAD protein signal transduction	17	23	3.943e-03
GO:BP	GO:0044804	nucleophagy	17	23	3.943e-03
GO:BP	GO:0170062	nutrient storage	51	93	4.005e-03
GO:BP	GO:0019915	lipid storage	51	93	4.005e-03
GO:BP	GO:0061951	establishment of protein localization to plasma membrane	38	65	4.043e-03
GO:BP	GO:0055013	cardiac muscle cell development	45	80	4.092e-03
GO:BP	GO:1903530	regulation of secretion by cell	248	563	4.132e-03
GO:BP	GO:0051293	establishment of spindle localization	37	63	4.230e-03
GO:BP	GO:0072526	pyridine-containing compound catabolic process	55	102	4.245e-03
GO:BP	GO:0042795	snRNA transcription by RNA polymerase II	13	16	4.252e-03
GO:BP	GO:0051607	defense response to virus	148	319	4.330e-03
GO:BP	GO:0070252	actin-mediated cell contraction	59	111	4.382e-03
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	232	524	4.396e-03
GO:BP	GO:0006695	cholesterol biosynthetic process	36	61	4.403e-03
GO:BP	GO:1902653	secondary alcohol biosynthetic process	36	61	4.403e-03
GO:BP	GO:0044090	positive regulation of vacuole organization	18	25	4.433e-03
GO:BP	GO:0070841	inclusion body assembly	18	25	4.433e-03
GO:BP	GO:1903779	regulation of cardiac conduction	18	25	4.433e-03
GO:BP	GO:0090257	regulation of muscle system process	111	231	4.471e-03
GO:BP	GO:1902893	regulation of miRNA transcription	43	76	4.561e-03
GO:BP	GO:0072132	mesenchyme morphogenesis	35	59	4.575e-03
GO:BP	GO:0086002	cardiac muscle cell action potential involved in contraction	35	59	4.575e-03
GO:BP	GO:0007254	JNK cascade	87	175	4.599e-03
GO:BP	GO:0042391	regulation of membrane potential	205	458	4.603e-03
GO:BP	GO:0051091	positive regulation of DNA-binding transcription factor activity	96	196	4.657e-03
GO:BP	GO:0048709	oligodendrocyte differentiation	58	109	4.657e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	364	854	4.704e-03
GO:BP	GO:0030865	cortical cytoskeleton organization	34	57	4.747e-03
GO:BP	GO:0051298	centrosome duplication	42	74	4.795e-03
GO:BP	GO:0071260	cellular response to mechanical stimulus	42	74	4.795e-03
GO:BP	GO:0032008	positive regulation of TOR signaling	42	74	4.795e-03
GO:BP	GO:0007018	microtubule-based movement	213	478	4.807e-03
GO:BP	GO:0071480	cellular response to gamma radiation	19	27	4.822e-03
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	19	27	4.822e-03
GO:BP	GO:0032511	late endosome to vacuole transport via multivesicular body sorting pathway	19	27	4.822e-03
GO:BP	GO:1903828	negative regulation of protein localization	104	215	4.878e-03
GO:BP	GO:0042158	lipoprotein biosynthetic process	33	55	4.898e-03
GO:BP	GO:0006220	pyrimidine nucleotide metabolic process	33	55	4.898e-03
GO:BP	GO:0009749	response to glucose	101	208	4.915e-03
GO:BP	GO:0007519	skeletal muscle tissue development	89	180	4.935e-03
GO:BP	GO:0031334	positive regulation of protein-containing complex assembly	98	201	4.940e-03
GO:BP	GO:0006936	muscle contraction	160	349	5.020e-03
GO:BP	GO:0051881	regulation of mitochondrial membrane potential	41	72	5.022e-03
GO:BP	GO:0051101	regulation of DNA binding	41	72	5.022e-03
GO:BP	GO:0051962	positive regulation of nervous system development	138	296	5.022e-03
GO:BP	GO:2000036	regulation of stem cell population maintenance	41	72	5.022e-03
GO:BP	GO:0001570	vasculogenesis	47	85	5.028e-03
GO:BP	GO:0051153	regulation of striated muscle cell differentiation	47	85	5.028e-03
GO:BP	GO:0034508	centromere complex assembly	20	29	5.123e-03
GO:BP	GO:0009649	entrainment of circadian clock	20	29	5.123e-03
GO:BP	GO:0002040	sprouting angiogenesis	68	132	5.248e-03
GO:BP	GO:0042273	ribosomal large subunit biogenesis	40	70	5.285e-03
GO:BP	GO:0097192	extrinsic apoptotic signaling pathway in absence of ligand	40	70	5.285e-03
GO:BP	GO:0090174	organelle membrane fusion	64	123	5.325e-03
GO:BP	GO:0043242	negative regulation of protein-containing complex disassembly	46	83	5.331e-03
GO:BP	GO:0097009	energy homeostasis	46	83	5.331e-03
GO:BP	GO:0006497	protein lipidation	30	49	5.336e-03
GO:BP	GO:0045724	positive regulation of cilium assembly	21	31	5.366e-03
GO:BP	GO:0032465	regulation of cytokinesis	51	94	5.377e-03
GO:BP	GO:0086066	atrial cardiac muscle cell to AV node cell communication	14	18	5.382e-03
GO:BP	GO:0086014	atrial cardiac muscle cell action potential	14	18	5.382e-03
GO:BP	GO:0086026	atrial cardiac muscle cell to AV node cell signaling	14	18	5.382e-03
GO:BP	GO:0051336	regulation of hydrolase activity	161	352	5.415e-03
GO:BP	GO:0006509	membrane protein ectodomain proteolysis	29	47	5.445e-03
GO:BP	GO:0043038	amino acid activation	29	47	5.445e-03
GO:BP	GO:0030307	positive regulation of cell growth	81	162	5.483e-03
GO:BP	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	139	299	5.484e-03
GO:BP	GO:0150116	regulation of cell-substrate junction organization	39	68	5.516e-03
GO:BP	GO:0051653	spindle localization	39	68	5.516e-03
GO:BP	GO:0051149	positive regulation of muscle cell differentiation	39	68	5.516e-03
GO:BP	GO:0051260	protein homooligomerization	99	204	5.556e-03
GO:BP	GO:0022612	gland morphogenesis	67	130	5.561e-03
GO:BP	GO:0046661	male sex differentiation	87	176	5.584e-03
GO:BP	GO:0140029	exocytic process	45	81	5.600e-03
GO:BP	GO:0000154	rRNA modification	23	35	5.600e-03
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	158	345	5.600e-03
GO:BP	GO:0048489	synaptic vesicle transport	27	43	5.600e-03
GO:BP	GO:0000462	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	23	35	5.600e-03
GO:BP	GO:0043276	anoikis	23	35	5.600e-03
GO:BP	GO:0007099	centriole replication	27	43	5.600e-03
GO:BP	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	63	121	5.613e-03
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	26	41	5.643e-03
GO:BP	GO:0003161	cardiac conduction system development	24	37	5.643e-03
GO:BP	GO:0031111	negative regulation of microtubule polymerization or depolymerization	26	41	5.643e-03
GO:BP	GO:0035330	regulation of hippo signaling	26	41	5.643e-03
GO:BP	GO:0003230	cardiac atrium development	24	37	5.643e-03
GO:BP	GO:0070979	protein K11-linked ubiquitination	25	39	5.648e-03
GO:BP	GO:0034389	lipid droplet organization	25	39	5.648e-03
GO:BP	GO:1905898	positive regulation of response to endoplasmic reticulum stress	25	39	5.648e-03
GO:BP	GO:0097120	receptor localization to synapse	44	79	5.902e-03
GO:BP	GO:0017157	regulation of exocytosis	89	181	5.960e-03
GO:BP	GO:0070555	response to interleukin-1	58	110	5.992e-03
GO:BP	GO:0043470	regulation of carbohydrate catabolic process	37	64	6.035e-03
GO:BP	GO:0016447	somatic recombination of immunoglobulin gene segments	37	64	6.035e-03
GO:BP	GO:0001682	tRNA 5’-leader removal	11	13	6.201e-03
GO:BP	GO:0018107	peptidyl-threonine phosphorylation	43	77	6.258e-03
GO:BP	GO:0019364	pyridine nucleotide catabolic process	53	99	6.282e-03
GO:BP	GO:0051963	regulation of synapse assembly	82	165	6.306e-03
GO:BP	GO:0051148	negative regulation of muscle cell differentiation	36	62	6.330e-03
GO:BP	GO:0045010	actin nucleation	36	62	6.330e-03
GO:BP	GO:0006098	pentose-phosphate shunt	15	20	6.363e-03
GO:BP	GO:0060716	labyrinthine layer blood vessel development	15	20	6.363e-03
GO:BP	GO:0048588	developmental cell growth	108	226	6.370e-03
GO:BP	GO:0044272	sulfur compound biosynthetic process	75	149	6.532e-03
GO:BP	GO:0071496	cellular response to external stimulus	42	75	6.618e-03
GO:BP	GO:0060420	regulation of heart growth	35	60	6.630e-03
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	78	156	6.655e-03
GO:BP	GO:0008015	blood circulation	228	518	6.728e-03
GO:BP	GO:0048864	stem cell development	47	86	6.791e-03
GO:BP	GO:0014897	striated muscle hypertrophy	47	86	6.791e-03
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	234	533	6.836e-03
GO:BP	GO:0030166	proteoglycan biosynthetic process	41	73	7.004e-03
GO:BP	GO:0016042	lipid catabolic process	161	354	7.124e-03
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	51	95	7.145e-03
GO:BP	GO:0034612	response to tumor necrosis factor	109	229	7.146e-03
GO:BP	GO:1900542	regulation of purine nucleotide metabolic process	46	84	7.233e-03
GO:BP	GO:0032211	negative regulation of telomere maintenance via telomerase	16	22	7.256e-03
GO:BP	GO:0035493	SNARE complex assembly	16	22	7.256e-03
GO:BP	GO:0044794	positive regulation by host of viral process	16	22	7.256e-03
GO:BP	GO:2001235	positive regulation of apoptotic signaling pathway	70	138	7.292e-03
GO:BP	GO:0007040	lysosome organization	59	113	7.302e-03
GO:BP	GO:0080171	lytic vacuole organization	59	113	7.302e-03
GO:BP	GO:0120034	positive regulation of plasma membrane bounded cell projection assembly	59	113	7.302e-03
GO:BP	GO:0071356	cellular response to tumor necrosis factor	100	208	7.520e-03
GO:BP	GO:0006110	regulation of glycolytic process	32	54	7.520e-03
GO:BP	GO:0033121	regulation of purine nucleotide catabolic process	32	54	7.520e-03
GO:BP	GO:0030811	regulation of nucleotide catabolic process	32	54	7.520e-03
GO:BP	GO:0008584	male gonad development	76	152	7.614e-03
GO:BP	GO:0009416	response to light stimulus	148	323	7.665e-03
GO:BP	GO:0060538	skeletal muscle organ development	94	194	7.691e-03
GO:BP	GO:0030048	actin filament-based movement	69	136	7.778e-03
GO:BP	GO:0043467	regulation of generation of precursor metabolites and energy	69	136	7.778e-03
GO:BP	GO:0016925	protein sumoylation	39	69	7.778e-03
GO:BP	GO:0016052	carbohydrate catabolic process	85	173	7.778e-03
GO:BP	GO:0016126	sterol biosynthetic process	39	69	7.778e-03
GO:BP	GO:0006066	alcohol metabolic process	164	362	7.791e-03
GO:BP	GO:0051216	cartilage development	102	213	7.882e-03
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	133	287	7.885e-03
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	17	24	7.928e-03
GO:BP	GO:0072273	metanephric nephron morphogenesis	17	24	7.928e-03
GO:BP	GO:0007042	lysosomal lumen acidification	17	24	7.928e-03
GO:BP	GO:0060038	cardiac muscle cell proliferation	30	50	8.084e-03
GO:BP	GO:0014032	neural crest cell development	44	80	8.100e-03
GO:BP	GO:0032271	regulation of protein polymerization	96	199	8.100e-03
GO:BP	GO:0008593	regulation of Notch signaling pathway	53	100	8.277e-03
GO:BP	GO:0140467	integrated stress response signaling	29	48	8.369e-03
GO:BP	GO:0043408	regulation of MAPK cascade	275	637	8.372e-03
GO:BP	GO:1904507	positive regulation of telomere maintenance in response to DNA damage	12	15	8.436e-03
GO:BP	GO:0034616	response to laminar fluid shear stress	12	15	8.436e-03
GO:BP	GO:0015937	coenzyme A biosynthetic process	9	10	8.436e-03
GO:BP	GO:0031125	rRNA 3’-end processing	9	10	8.436e-03
GO:BP	GO:0110025	DNA strand resection involved in replication fork processing	9	10	8.436e-03
GO:BP	GO:0018216	peptidyl-arginine methylation	9	10	8.436e-03
GO:BP	GO:0031167	rRNA methylation	18	26	8.464e-03
GO:BP	GO:0046339	diacylglycerol metabolic process	18	26	8.464e-03
GO:BP	GO:0002831	regulation of response to biotic stimulus	236	540	8.494e-03
GO:BP	GO:0050679	positive regulation of epithelial cell proliferation	98	204	8.507e-03
GO:BP	GO:0051057	positive regulation of small GTPase mediated signal transduction	43	78	8.569e-03
GO:BP	GO:0043039	tRNA aminoacylation	28	46	8.578e-03
GO:BP	GO:0048705	skeletal system morphogenesis	111	235	8.768e-03
GO:BP	GO:0043583	ear development	111	235	8.768e-03
GO:BP	GO:2000300	regulation of synaptic vesicle exocytosis	27	44	8.811e-03
GO:BP	GO:0060338	regulation of type I interferon-mediated signaling pathway	27	44	8.811e-03
GO:BP	GO:0045646	regulation of erythrocyte differentiation	27	44	8.811e-03
GO:BP	GO:0009134	nucleoside diphosphate catabolic process	56	107	8.833e-03
GO:BP	GO:0032801	receptor catabolic process	19	28	8.840e-03
GO:BP	GO:0003272	endocardial cushion formation	19	28	8.840e-03
GO:BP	GO:0003209	cardiac atrium morphogenesis	19	28	8.840e-03
GO:BP	GO:0006476	protein deacetylation	26	42	8.998e-03
GO:BP	GO:0019432	triglyceride biosynthetic process	26	42	8.998e-03
GO:BP	GO:0036297	interstrand cross-link repair	26	42	8.998e-03
GO:BP	GO:0046048	UDP metabolic process	7	7	9.032e-03
GO:BP	GO:0007221	positive regulation of transcription of Notch receptor target	7	7	9.032e-03
GO:BP	GO:2000638	regulation of SREBP signaling pathway	7	7	9.032e-03
GO:BP	GO:0045054	constitutive secretory pathway	7	7	9.032e-03
GO:BP	GO:0009193	pyrimidine ribonucleoside diphosphate metabolic process	7	7	9.032e-03
GO:BP	GO:0018023	peptidyl-lysine trimethylation	7	7	9.032e-03
GO:BP	GO:0035891	exit from host cell	20	30	9.072e-03
GO:BP	GO:0008535	respiratory chain complex IV assembly	20	30	9.072e-03
GO:BP	GO:0019076	viral release from host cell	20	30	9.072e-03
GO:BP	GO:0046660	female sex differentiation	63	123	9.072e-03
GO:BP	GO:1902686	mitochondrial outer membrane permeabilization involved in programmed cell death	25	40	9.112e-03
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	25	40	9.112e-03
GO:BP	GO:0032535	regulation of cellular component size	161	356	9.162e-03
GO:BP	GO:1902110	positive regulation of mitochondrial membrane permeability involved in apoptotic process	24	38	9.206e-03
GO:BP	GO:0071108	protein K48-linked deubiquitination	21	32	9.206e-03
GO:BP	GO:0000966	RNA 5’-end processing	24	38	9.206e-03
GO:BP	GO:0060043	regulation of cardiac muscle cell proliferation	24	38	9.206e-03
GO:BP	GO:1903955	positive regulation of protein targeting to mitochondrion	21	32	9.206e-03
GO:BP	GO:2000279	negative regulation of DNA biosynthetic process	21	32	9.206e-03
GO:BP	GO:0046546	development of primary male sexual characteristics	76	153	9.240e-03
GO:BP	GO:0106106	cold-induced thermogenesis	76	153	9.240e-03
GO:BP	GO:1903749	positive regulation of establishment of protein localization to mitochondrion	23	36	9.262e-03
GO:BP	GO:0086005	ventricular cardiac muscle cell action potential	22	34	9.262e-03
GO:BP	GO:0051348	negative regulation of transferase activity	82	167	9.321e-03
GO:BP	GO:0071709	membrane assembly	35	61	9.396e-03
GO:BP	GO:0006487	protein N-linked glycosylation	41	74	9.498e-03
GO:BP	GO:1902017	regulation of cilium assembly	41	74	9.498e-03
GO:BP	GO:0050801	monoatomic ion homeostasis	266	616	9.520e-03
GO:BP	GO:0055080	monoatomic cation homeostasis	262	606	9.520e-03
GO:BP	GO:0006140	regulation of nucleotide metabolic process	46	85	9.528e-03
GO:BP	GO:0048593	camera-type eye morphogenesis	69	137	9.555e-03
GO:BP	GO:0006906	vesicle fusion	62	121	9.626e-03
GO:BP	GO:0032648	regulation of interferon-beta production	34	59	9.865e-03
GO:BP	GO:0032608	interferon-beta production	34	59	9.865e-03
GO:BP	GO:0070646	protein modification by small protein removal	75	151	9.865e-03
GO:BP	GO:0043409	negative regulation of MAPK cascade	78	158	9.922e-03
GO:BP	GO:0007029	endoplasmic reticulum organization	54	103	9.922e-03
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	54	103	9.922e-03
GO:BP	GO:0002181	cytoplasmic translation	81	165	9.941e-03
GO:BP	GO:0061180	mammary gland epithelium development	40	72	1.004e-02
GO:BP	GO:0038034	signal transduction in absence of ligand	40	72	1.004e-02
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	45	83	1.013e-02
GO:BP	GO:0060382	regulation of DNA strand elongation	13	17	1.018e-02
GO:BP	GO:0032510	endosome to lysosome transport via multivesicular body sorting pathway	13	17	1.018e-02
GO:BP	GO:0051382	kinetochore assembly	13	17	1.018e-02
GO:BP	GO:0070131	positive regulation of mitochondrial translation	13	17	1.018e-02
GO:BP	GO:0051055	negative regulation of lipid biosynthetic process	33	57	1.031e-02
GO:BP	GO:0007062	sister chromatid cohesion	33	57	1.031e-02
GO:BP	GO:1902895	positive regulation of miRNA transcription	33	57	1.031e-02
GO:BP	GO:0007623	circadian rhythm	100	210	1.047e-02
GO:BP	GO:0090066	regulation of anatomical structure size	219	500	1.058e-02
GO:BP	GO:0110020	regulation of actomyosin structure organization	53	101	1.058e-02
GO:BP	GO:0032922	circadian regulation of gene expression	39	70	1.062e-02
GO:BP	GO:0009612	response to mechanical stimulus	105	222	1.069e-02
GO:BP	GO:0046328	regulation of JNK cascade	70	140	1.116e-02
GO:BP	GO:0007422	peripheral nervous system development	48	90	1.120e-02
GO:BP	GO:0051651	maintenance of location in cell	99	208	1.121e-02
GO:BP	GO:0043149	stress fiber assembly	56	108	1.124e-02
GO:BP	GO:0035282	segmentation	56	108	1.124e-02
GO:BP	GO:0030038	contractile actin filament bundle assembly	56	108	1.124e-02
GO:BP	GO:0051646	mitochondrion localization	31	53	1.134e-02
GO:BP	GO:0030100	regulation of endocytosis	136	297	1.163e-02
GO:BP	GO:0045637	regulation of myeloid cell differentiation	101	213	1.171e-02
GO:BP	GO:0009746	response to hexose	101	213	1.171e-02
GO:BP	GO:0035720	intraciliary anterograde transport	14	19	1.179e-02
GO:BP	GO:0021692	cerebellar Purkinje cell layer morphogenesis	14	19	1.179e-02
GO:BP	GO:0031053	primary miRNA processing	14	19	1.179e-02
GO:BP	GO:0097320	plasma membrane tubulation	14	19	1.179e-02
GO:BP	GO:0046579	positive regulation of Ras protein signal transduction	14	19	1.179e-02
GO:BP	GO:0051051	negative regulation of transport	183	412	1.184e-02
GO:BP	GO:0001892	embryonic placenta development	47	88	1.190e-02
GO:BP	GO:0014896	muscle hypertrophy	47	88	1.190e-02
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	69	138	1.190e-02
GO:BP	GO:0051235	maintenance of location	103	218	1.218e-02
GO:BP	GO:0033120	positive regulation of RNA splicing	29	49	1.235e-02
GO:BP	GO:0071526	semaphorin-plexin signaling pathway	29	49	1.235e-02
GO:BP	GO:0033674	positive regulation of kinase activity	118	254	1.238e-02
GO:BP	GO:0016051	carbohydrate biosynthetic process	92	192	1.240e-02
GO:BP	GO:0061723	glycophagy	10	12	1.267e-02
GO:BP	GO:0003207	cardiac chamber formation	10	12	1.267e-02
GO:BP	GO:0072710	response to hydroxyurea	10	12	1.267e-02
GO:BP	GO:1903671	negative regulation of sprouting angiogenesis	10	12	1.267e-02
GO:BP	GO:0060623	regulation of chromosome condensation	10	12	1.267e-02
GO:BP	GO:1905456	regulation of lymphoid progenitor cell differentiation	10	12	1.267e-02
GO:BP	GO:0042276	error-prone translesion synthesis	10	12	1.267e-02
GO:BP	GO:0086067	AV node cell to bundle of His cell communication	10	12	1.267e-02
GO:BP	GO:0033540	fatty acid beta-oxidation using acyl-CoA oxidase	10	12	1.267e-02
GO:BP	GO:1903441	protein localization to ciliary membrane	10	12	1.267e-02
GO:BP	GO:0047496	vesicle transport along microtubule	28	47	1.279e-02
GO:BP	GO:0046031	ADP metabolic process	54	104	1.279e-02
GO:BP	GO:0032365	intracellular lipid transport	28	47	1.279e-02
GO:BP	GO:0036465	synaptic vesicle recycling	50	95	1.284e-02
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	41	75	1.289e-02
GO:BP	GO:0007369	gastrulation	94	197	1.293e-02
GO:BP	GO:0099188	postsynaptic cytoskeleton organization	15	21	1.299e-02
GO:BP	GO:0006611	protein export from nucleus	35	62	1.326e-02
GO:BP	GO:0044786	cell cycle DNA replication	27	45	1.328e-02
GO:BP	GO:0046390	ribose phosphate biosynthetic process	88	183	1.340e-02
GO:BP	GO:0071347	cellular response to interleukin-1	45	84	1.350e-02
GO:BP	GO:0060759	regulation of response to cytokine stimulus	85	176	1.358e-02
GO:BP	GO:0072164	mesonephric tubule development	53	102	1.365e-02
GO:BP	GO:0005976	polysaccharide metabolic process	53	102	1.365e-02
GO:BP	GO:0072163	mesonephric epithelium development	53	102	1.365e-02
GO:BP	GO:1901880	negative regulation of protein depolymerization	40	73	1.369e-02
GO:BP	GO:1904888	cranial skeletal system development	40	73	1.369e-02
GO:BP	GO:0014033	neural crest cell differentiation	49	93	1.369e-02
GO:BP	GO:0045740	positive regulation of DNA replication	26	43	1.370e-02
GO:BP	GO:0071887	leukocyte apoptotic process	60	118	1.386e-02
GO:BP	GO:0006740	NADPH regeneration	16	23	1.388e-02
GO:BP	GO:0032401	establishment of melanosome localization	16	23	1.388e-02
GO:BP	GO:0045540	regulation of cholesterol biosynthetic process	16	23	1.388e-02
GO:BP	GO:0003283	atrial septum development	16	23	1.388e-02
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	16	23	1.388e-02
GO:BP	GO:0000963	mitochondrial RNA processing	16	23	1.388e-02
GO:BP	GO:0106118	regulation of sterol biosynthetic process	16	23	1.388e-02
GO:BP	GO:0051302	regulation of cell division	90	188	1.400e-02
GO:BP	GO:0006739	NADP metabolic process	25	41	1.410e-02
GO:BP	GO:0002221	pattern recognition receptor signaling pathway	123	267	1.417e-02
GO:BP	GO:0070897	transcription preinitiation complex assembly	44	82	1.431e-02
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	17	25	1.443e-02
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	24	39	1.443e-02
GO:BP	GO:0033143	regulation of intracellular steroid hormone receptor signaling pathway	39	71	1.443e-02
GO:BP	GO:0086064	cell communication by electrical coupling involved in cardiac conduction	17	25	1.443e-02
GO:BP	GO:0035020	regulation of Rac protein signal transduction	17	25	1.443e-02
GO:BP	GO:1901028	regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	17	25	1.443e-02
GO:BP	GO:0007031	peroxisome organization	24	39	1.443e-02
GO:BP	GO:0009137	purine nucleoside diphosphate catabolic process	52	100	1.443e-02
GO:BP	GO:0051125	regulation of actin nucleation	24	39	1.443e-02
GO:BP	GO:0035994	response to muscle stretch	17	25	1.443e-02
GO:BP	GO:0032400	melanosome localization	17	25	1.443e-02
GO:BP	GO:0009181	purine ribonucleoside diphosphate catabolic process	52	100	1.443e-02
GO:BP	GO:0046677	response to antibiotic	24	39	1.443e-02
GO:BP	GO:0099622	cardiac muscle cell membrane repolarization	24	39	1.443e-02
GO:BP	GO:0055088	lipid homeostasis	81	167	1.443e-02
GO:BP	GO:0050673	epithelial cell proliferation	194	441	1.443e-02
GO:BP	GO:2000780	negative regulation of double-strand break repair	24	39	1.443e-02
GO:BP	GO:0090181	regulation of cholesterol metabolic process	24	39	1.443e-02
GO:BP	GO:0097150	neuronal stem cell population maintenance	17	25	1.443e-02
GO:BP	GO:0071396	cellular response to lipid	263	613	1.446e-02
GO:BP	GO:0051017	actin filament bundle assembly	78	160	1.452e-02
GO:BP	GO:0048278	vesicle docking	33	58	1.453e-02
GO:BP	GO:0050770	regulation of axonogenesis	72	146	1.454e-02
GO:BP	GO:0016233	telomere capping	18	27	1.486e-02
GO:BP	GO:0010882	regulation of cardiac muscle contraction by calcium ion signaling	18	27	1.486e-02
GO:BP	GO:0043537	negative regulation of blood vessel endothelial cell migration	22	35	1.492e-02
GO:BP	GO:0046320	regulation of fatty acid oxidation	22	35	1.492e-02
GO:BP	GO:0060384	innervation	19	29	1.501e-02
GO:BP	GO:0002063	chondrocyte development	21	33	1.501e-02
GO:BP	GO:0061842	microtubule organizing center localization	21	33	1.501e-02
GO:BP	GO:0021680	cerebellar Purkinje cell layer development	19	29	1.501e-02
GO:BP	GO:1902473	regulation of protein localization to synapse	19	29	1.501e-02
GO:BP	GO:0034250	positive regulation of amide metabolic process	19	29	1.501e-02
GO:BP	GO:0051642	centrosome localization	21	33	1.501e-02
GO:BP	GO:0060964	regulation of miRNA-mediated gene silencing	19	29	1.501e-02
GO:BP	GO:0030510	regulation of BMP signaling pathway	55	107	1.501e-02
GO:BP	GO:0009218	pyrimidine ribonucleotide metabolic process	21	33	1.501e-02
GO:BP	GO:0010644	cell communication by electrical coupling	21	33	1.501e-02
GO:BP	GO:0009165	nucleotide biosynthetic process	107	229	1.502e-02
GO:BP	GO:1900101	regulation of endoplasmic reticulum unfolded protein response	20	31	1.503e-02
GO:BP	GO:0007064	mitotic sister chromatid cohesion	20	31	1.503e-02
GO:BP	GO:0098868	bone growth	20	31	1.503e-02
GO:BP	GO:0060147	regulation of post-transcriptional gene silencing	20	31	1.503e-02
GO:BP	GO:0002204	somatic recombination of immunoglobulin genes involved in immune response	32	56	1.512e-02
GO:BP	GO:0002208	somatic diversification of immunoglobulins involved in immune response	32	56	1.512e-02
GO:BP	GO:0010718	positive regulation of epithelial to mesenchymal transition	32	56	1.512e-02
GO:BP	GO:0045190	isotype switching	32	56	1.512e-02
GO:BP	GO:0071470	cellular response to osmotic stress	32	56	1.512e-02
GO:BP	GO:0042987	amyloid precursor protein catabolic process	32	56	1.512e-02
GO:BP	GO:0006473	protein acetylation	32	56	1.512e-02
GO:BP	GO:0062237	protein localization to postsynapse	32	56	1.512e-02
GO:BP	GO:0001959	regulation of cytokine-mediated signaling pathway	80	165	1.522e-02
GO:BP	GO:0006470	protein dephosphorylation	71	144	1.538e-02
GO:BP	GO:0120161	regulation of cold-induced thermogenesis	74	151	1.538e-02
GO:BP	GO:0043393	regulation of protein binding	58	114	1.545e-02
GO:BP	GO:0002062	chondrocyte differentiation	61	121	1.591e-02
GO:BP	GO:0045911	positive regulation of DNA recombination	42	78	1.591e-02
GO:BP	GO:0060324	face development	31	54	1.593e-02
GO:BP	GO:0021695	cerebellar cortex development	31	54	1.593e-02
GO:BP	GO:0055021	regulation of cardiac muscle tissue growth	31	54	1.593e-02
GO:BP	GO:0098734	macromolecule depalmitoylation	11	14	1.600e-02
GO:BP	GO:0051775	response to redox state	11	14	1.600e-02
GO:BP	GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation	11	14	1.600e-02
GO:BP	GO:1901985	positive regulation of protein acetylation	11	14	1.600e-02
GO:BP	GO:1990845	adaptive thermogenesis	82	170	1.606e-02
GO:BP	GO:0030282	bone mineralization	64	128	1.614e-02
GO:BP	GO:0140238	presynaptic endocytosis	46	87	1.621e-02
GO:BP	GO:0061572	actin filament bundle organization	79	163	1.623e-02
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	57	112	1.652e-02
GO:BP	GO:0003197	endocardial cushion development	30	52	1.673e-02
GO:BP	GO:0097300	programmed necrotic cell death	30	52	1.673e-02
GO:BP	GO:1904377	positive regulation of protein localization to cell periphery	41	76	1.692e-02
GO:BP	GO:2000630	positive regulation of miRNA metabolic process	36	65	1.693e-02
GO:BP	GO:0046824	positive regulation of nucleocytoplasmic transport	36	65	1.693e-02
GO:BP	GO:0061053	somite development	45	85	1.735e-02
GO:BP	GO:0060021	roof of mouth development	49	94	1.735e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	138	305	1.736e-02
GO:BP	GO:0043523	regulation of neuron apoptotic process	112	242	1.740e-02
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	112	242	1.740e-02
GO:BP	GO:0006639	acylglycerol metabolic process	66	133	1.748e-02
GO:BP	GO:0072073	kidney epithelium development	75	154	1.751e-02
GO:BP	GO:0043622	cortical microtubule organization	8	9	1.763e-02
GO:BP	GO:0031946	regulation of glucocorticoid biosynthetic process	8	9	1.763e-02
GO:BP	GO:0062176	R-loop processing	8	9	1.763e-02
GO:BP	GO:0042532	negative regulation of tyrosine phosphorylation of STAT protein	8	9	1.763e-02
GO:BP	GO:0009138	pyrimidine nucleoside diphosphate metabolic process	8	9	1.763e-02
GO:BP	GO:0140673	transcription elongation-coupled chromatin remodeling	8	9	1.763e-02
GO:BP	GO:0097680	double-strand break repair via classical nonhomologous end joining	8	9	1.763e-02
GO:BP	GO:1904874	positive regulation of telomerase RNA localization to Cajal body	8	9	1.763e-02
GO:BP	GO:0009200	deoxyribonucleoside triphosphate metabolic process	8	9	1.763e-02
GO:BP	GO:0046602	regulation of mitotic centrosome separation	8	9	1.763e-02
GO:BP	GO:0001657	ureteric bud development	52	101	1.818e-02
GO:BP	GO:1902459	positive regulation of stem cell population maintenance	28	48	1.835e-02
GO:BP	GO:0034314	Arp2/3 complex-mediated actin nucleation	28	48	1.835e-02
GO:BP	GO:0120163	negative regulation of cold-induced thermogenesis	28	48	1.835e-02
GO:BP	GO:0060443	mammary gland morphogenesis	28	48	1.835e-02
GO:BP	GO:0048488	synaptic vesicle endocytosis	44	83	1.841e-02
GO:BP	GO:0072028	nephron morphogenesis	44	83	1.841e-02
GO:BP	GO:0051899	membrane depolarization	48	92	1.844e-02
GO:BP	GO:0001659	temperature homeostasis	88	185	1.852e-02
GO:BP	GO:0072522	purine-containing compound biosynthetic process	118	257	1.872e-02
GO:BP	GO:0048313	Golgi inheritance	12	16	1.884e-02
GO:BP	GO:0048308	organelle inheritance	12	16	1.884e-02
GO:BP	GO:0043328	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	12	16	1.884e-02
GO:BP	GO:0030242	autophagy of peroxisome	12	16	1.884e-02
GO:BP	GO:0051299	centrosome separation	12	16	1.884e-02
GO:BP	GO:1903358	regulation of Golgi organization	12	16	1.884e-02
GO:BP	GO:0098693	regulation of synaptic vesicle cycle	12	16	1.884e-02
GO:BP	GO:1900034	regulation of cellular response to heat	12	16	1.884e-02
GO:BP	GO:0099116	tRNA 5’-end processing	12	16	1.884e-02
GO:BP	GO:1900076	regulation of cellular response to insulin stimulus	39	72	1.903e-02
GO:BP	GO:1902041	regulation of extrinsic apoptotic signaling pathway via death domain receptors	27	46	1.911e-02
GO:BP	GO:1905710	positive regulation of membrane permeability	27	46	1.911e-02
GO:BP	GO:0023061	signal release	217	501	1.913e-02
GO:BP	GO:0055085	transmembrane transport	639	1578	1.914e-02
GO:BP	GO:0043524	negative regulation of neuron apoptotic process	79	164	1.945e-02
GO:BP	GO:0030323	respiratory tube development	95	202	1.952e-02
GO:BP	GO:0097581	lamellipodium organization	47	90	1.964e-02
GO:BP	GO:0008361	regulation of cell size	87	183	1.969e-02
GO:BP	GO:0045834	positive regulation of lipid metabolic process	64	129	1.986e-02
GO:BP	GO:0034205	amyloid-beta formation	26	44	1.997e-02
GO:BP	GO:0061462	protein localization to lysosome	33	59	2.000e-02
GO:BP	GO:0061326	renal tubule development	54	106	2.006e-02
GO:BP	GO:0001823	mesonephros development	54	106	2.006e-02
GO:BP	GO:0009260	ribonucleotide biosynthetic process	84	176	2.008e-02
GO:BP	GO:0060415	muscle tissue morphogenesis	38	70	2.021e-02
GO:BP	GO:0048645	animal organ formation	38	70	2.021e-02
GO:BP	GO:0045669	positive regulation of osteoblast differentiation	38	70	2.021e-02
GO:BP	GO:0002064	epithelial cell development	102	219	2.024e-02
GO:BP	GO:0033135	regulation of peptidyl-serine phosphorylation	50	97	2.054e-02
GO:BP	GO:0032471	negative regulation of endoplasmic reticulum calcium ion concentration	6	6	2.054e-02
GO:BP	GO:0046032	ADP catabolic process	50	97	2.054e-02
GO:BP	GO:0031999	negative regulation of fatty acid beta-oxidation	6	6	2.054e-02
GO:BP	GO:0014031	mesenchymal cell development	6	6	2.054e-02
GO:BP	GO:1904760	regulation of myofibroblast differentiation	6	6	2.054e-02
GO:BP	GO:1901858	regulation of mitochondrial DNA metabolic process	6	6	2.054e-02
GO:BP	GO:0090316	positive regulation of intracellular protein transport	50	97	2.054e-02
GO:BP	GO:0015961	diadenosine polyphosphate catabolic process	6	6	2.054e-02
GO:BP	GO:0046929	negative regulation of neurotransmitter secretion	6	6	2.054e-02
GO:BP	GO:0031087	deadenylation-independent decapping of nuclear-transcribed mRNA	6	6	2.054e-02
GO:BP	GO:0003415	chondrocyte hypertrophy	6	6	2.054e-02
GO:BP	GO:0042791	5S class rRNA transcription by RNA polymerase III	6	6	2.054e-02
GO:BP	GO:0046368	GDP-L-fucose metabolic process	6	6	2.054e-02
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	25	42	2.062e-02
GO:BP	GO:0043923	positive regulation by host of viral transcription	13	18	2.090e-02
GO:BP	GO:0034727	piecemeal microautophagy of the nucleus	13	18	2.090e-02
GO:BP	GO:0015936	coenzyme A metabolic process	13	18	2.090e-02
GO:BP	GO:0007096	regulation of exit from mitosis	13	18	2.090e-02
GO:BP	GO:0072087	renal vesicle development	13	18	2.090e-02
GO:BP	GO:0032239	regulation of nucleobase-containing compound transport	13	18	2.090e-02
GO:BP	GO:0006638	neutral lipid metabolic process	66	134	2.115e-02
GO:BP	GO:1903115	regulation of actin filament-based movement	24	40	2.140e-02
GO:BP	GO:0060391	positive regulation of SMAD protein signal transduction	24	40	2.140e-02
GO:BP	GO:0070266	necroptotic process	24	40	2.140e-02
GO:BP	GO:0006096	glycolytic process	49	95	2.196e-02
GO:BP	GO:0030324	lung development	93	198	2.202e-02
GO:BP	GO:0048286	lung alveolus development	31	55	2.219e-02
GO:BP	GO:0045023	G0 to G1 transition	23	38	2.219e-02
GO:BP	GO:0000271	polysaccharide biosynthetic process	31	55	2.219e-02
GO:BP	GO:0046473	phosphatidic acid metabolic process	23	38	2.219e-02
GO:BP	GO:1903539	protein localization to postsynaptic membrane	31	55	2.219e-02
GO:BP	GO:0045860	positive regulation of protein kinase activity	110	239	2.250e-02
GO:BP	GO:0042407	cristae formation	14	20	2.251e-02
GO:BP	GO:0061003	positive regulation of dendritic spine morphogenesis	14	20	2.251e-02
GO:BP	GO:0010866	regulation of triglyceride biosynthetic process	14	20	2.251e-02
GO:BP	GO:0002097	tRNA wobble base modification	14	20	2.251e-02
GO:BP	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	14	20	2.251e-02
GO:BP	GO:0007368	determination of left/right symmetry	68	139	2.257e-02
GO:BP	GO:0043604	amide biosynthetic process	82	172	2.266e-02
GO:BP	GO:0006904	vesicle docking involved in exocytosis	22	36	2.285e-02
GO:BP	GO:0070316	regulation of G0 to G1 transition	22	36	2.285e-02
GO:BP	GO:0002218	activation of innate immune response	137	305	2.341e-02
GO:BP	GO:0060914	heart formation	21	34	2.341e-02
GO:BP	GO:0120009	intermembrane lipid transfer	21	34	2.341e-02
GO:BP	GO:0034405	response to fluid shear stress	21	34	2.341e-02
GO:BP	GO:2000677	regulation of transcription regulatory region DNA binding	21	34	2.341e-02
GO:BP	GO:0097345	mitochondrial outer membrane permeabilization	21	34	2.341e-02
GO:BP	GO:0051654	establishment of mitochondrion localization	21	34	2.341e-02
GO:BP	GO:0006734	NADH metabolic process	21	34	2.341e-02
GO:BP	GO:0090169	regulation of spindle assembly	21	34	2.341e-02
GO:BP	GO:0086009	membrane repolarization	30	53	2.341e-02
GO:BP	GO:0019083	viral transcription	30	53	2.341e-02
GO:BP	GO:0050678	regulation of epithelial cell proliferation	161	364	2.343e-02
GO:BP	GO:0032402	melanosome transport	15	22	2.343e-02
GO:BP	GO:0009083	branched-chain amino acid catabolic process	15	22	2.343e-02
GO:BP	GO:0016082	synaptic vesicle priming	15	22	2.343e-02
GO:BP	GO:0034472	snRNA 3’-end processing	15	22	2.343e-02
GO:BP	GO:0000212	meiotic spindle organization	15	22	2.343e-02
GO:BP	GO:0021756	striatum development	15	22	2.343e-02
GO:BP	GO:0008090	retrograde axonal transport	15	22	2.343e-02
GO:BP	GO:0003228	atrial cardiac muscle tissue development	15	22	2.343e-02
GO:BP	GO:0005977	glycogen metabolic process	44	84	2.352e-02
GO:BP	GO:0006970	response to osmotic stress	44	84	2.352e-02
GO:BP	GO:0090317	negative regulation of intracellular protein transport	20	32	2.375e-02
GO:BP	GO:0061036	positive regulation of cartilage development	20	32	2.375e-02
GO:BP	GO:0009306	protein secretion	167	379	2.375e-02
GO:BP	GO:0099022	vesicle tethering	20	32	2.375e-02
GO:BP	GO:0006622	protein targeting to lysosome	20	32	2.375e-02
GO:BP	GO:0035751	regulation of lysosomal lumen pH	20	32	2.375e-02
GO:BP	GO:0060966	regulation of gene silencing by regulatory ncRNA	20	32	2.375e-02
GO:BP	GO:0014887	cardiac muscle adaptation	16	24	2.392e-02
GO:BP	GO:1901673	regulation of mitotic spindle assembly	16	24	2.392e-02
GO:BP	GO:0051905	establishment of pigment granule localization	16	24	2.392e-02
GO:BP	GO:1902993	positive regulation of amyloid precursor protein catabolic process	16	24	2.392e-02
GO:BP	GO:0009147	pyrimidine nucleoside triphosphate metabolic process	16	24	2.392e-02
GO:BP	GO:0014898	cardiac muscle hypertrophy in response to stress	16	24	2.392e-02
GO:BP	GO:0043153	entrainment of circadian clock by photoperiod	16	24	2.392e-02
GO:BP	GO:0003299	muscle hypertrophy in response to stress	16	24	2.392e-02
GO:BP	GO:0009266	response to temperature stimulus	81	170	2.392e-02
GO:BP	GO:0060993	kidney morphogenesis	51	100	2.396e-02
GO:BP	GO:1900368	regulation of post-transcriptional gene silencing by regulatory ncRNA	19	30	2.402e-02
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	19	30	2.402e-02
GO:BP	GO:0042063	gliogenesis	156	352	2.405e-02
GO:BP	GO:0006760	folic acid-containing compound metabolic process	17	26	2.408e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	17	26	2.408e-02
GO:BP	GO:0034643	establishment of mitochondrion localization, microtubule-mediated	18	28	2.408e-02
GO:BP	GO:0098901	regulation of cardiac muscle cell action potential	18	28	2.408e-02
GO:BP	GO:2000819	regulation of nucleotide-excision repair	18	28	2.408e-02
GO:BP	GO:0033617	mitochondrial cytochrome c oxidase assembly	17	26	2.408e-02
GO:BP	GO:0009081	branched-chain amino acid metabolic process	18	28	2.408e-02
GO:BP	GO:0003416	endochondral bone growth	18	28	2.408e-02
GO:BP	GO:2000737	negative regulation of stem cell differentiation	17	26	2.408e-02
GO:BP	GO:0047497	mitochondrion transport along microtubule	18	28	2.408e-02
GO:BP	GO:0051875	pigment granule localization	17	26	2.408e-02
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	29	51	2.419e-02
GO:BP	GO:0062028	regulation of stress granule assembly	9	11	2.432e-02
GO:BP	GO:0071028	nuclear mRNA surveillance	9	11	2.432e-02
GO:BP	GO:0000290	deadenylation-dependent decapping of nuclear-transcribed mRNA	9	11	2.432e-02
GO:BP	GO:0030953	astral microtubule organization	9	11	2.432e-02
GO:BP	GO:0031943	regulation of glucocorticoid metabolic process	9	11	2.432e-02
GO:BP	GO:0010807	regulation of synaptic vesicle priming	9	11	2.432e-02
GO:BP	GO:0016311	dephosphorylation	101	218	2.432e-02
GO:BP	GO:0086070	SA node cell to atrial cardiac muscle cell communication	9	11	2.432e-02
GO:BP	GO:0046710	GDP metabolic process	9	11	2.432e-02
GO:BP	GO:0072697	protein localization to cell cortex	9	11	2.432e-02
GO:BP	GO:0072711	cellular response to hydroxyurea	9	11	2.432e-02
GO:BP	GO:0046834	lipid phosphorylation	9	11	2.432e-02
GO:BP	GO:0010595	positive regulation of endothelial cell migration	54	107	2.433e-02
GO:BP	GO:0040011	locomotion	512	1255	2.456e-02
GO:BP	GO:0009064	glutamine family amino acid metabolic process	43	82	2.467e-02
GO:BP	GO:0045088	regulation of innate immune response	195	449	2.468e-02
GO:BP	GO:0042752	regulation of circadian rhythm	57	114	2.478e-02
GO:BP	GO:0035592	establishment of protein localization to extracellular region	168	382	2.479e-02
GO:BP	GO:0003179	heart valve morphogenesis	34	62	2.495e-02
GO:BP	GO:0009161	ribonucleoside monophosphate metabolic process	34	62	2.495e-02
GO:BP	GO:0032387	negative regulation of intracellular transport	28	49	2.536e-02
GO:BP	GO:1903747	regulation of establishment of protein localization to mitochondrion	28	49	2.536e-02
GO:BP	GO:0006111	regulation of gluconeogenesis	28	49	2.536e-02
GO:BP	GO:0050890	cognition	146	328	2.562e-02
GO:BP	GO:0009743	response to carbohydrate	112	245	2.584e-02
GO:BP	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	53	105	2.607e-02
GO:BP	GO:0008589	regulation of smoothened signaling pathway	46	89	2.607e-02
GO:BP	GO:0000423	mitophagy	38	71	2.608e-02
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	42	80	2.637e-02
GO:BP	GO:0035914	skeletal muscle cell differentiation	42	80	2.637e-02
GO:BP	GO:0043124	negative regulation of canonical NF-kappaB signal transduction	33	60	2.657e-02
GO:BP	GO:0008360	regulation of cell shape	68	140	2.672e-02
GO:BP	GO:0010463	mesenchymal cell proliferation	27	47	2.675e-02
GO:BP	GO:0043255	regulation of carbohydrate biosynthetic process	49	96	2.716e-02
GO:BP	GO:0007272	ensheathment of neurons	76	159	2.742e-02
GO:BP	GO:0008366	axon ensheathment	76	159	2.742e-02
GO:BP	GO:0018210	peptidyl-threonine modification	45	87	2.790e-02
GO:BP	GO:0006879	intracellular iron ion homeostasis	37	69	2.790e-02
GO:BP	GO:0032231	regulation of actin filament bundle assembly	52	103	2.790e-02
GO:BP	GO:2000177	regulation of neural precursor cell proliferation	52	103	2.790e-02
GO:BP	GO:0060349	bone morphogenesis	52	103	2.790e-02
GO:BP	GO:1903825	organic acid transmembrane transport	73	152	2.790e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	394	954	2.790e-02
GO:BP	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	26	45	2.814e-02
GO:BP	GO:0018279	protein N-linked glycosylation via asparagine	26	45	2.814e-02
GO:BP	GO:0048644	muscle organ morphogenesis	41	78	2.817e-02
GO:BP	GO:0001101	response to acid chemical	70	145	2.822e-02
GO:BP	GO:0033673	negative regulation of kinase activity	70	145	2.822e-02
GO:BP	GO:0098739	import across plasma membrane	91	195	2.849e-02
GO:BP	GO:0043200	response to amino acid	64	131	2.875e-02
GO:BP	GO:0034762	regulation of transmembrane transport	192	443	2.875e-02
GO:BP	GO:0031347	regulation of defense response	337	809	2.892e-02
GO:BP	GO:0042552	myelination	75	157	2.925e-02
GO:BP	GO:0007595	lactation	25	43	2.953e-02
GO:BP	GO:0072528	pyrimidine-containing compound biosynthetic process	25	43	2.953e-02
GO:BP	GO:1902175	regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	25	43	2.953e-02
GO:BP	GO:0006418	tRNA aminoacylation for protein translation	25	43	2.953e-02
GO:BP	GO:1903214	regulation of protein targeting to mitochondrion	25	43	2.953e-02
GO:BP	GO:0046626	regulation of insulin receptor signaling pathway	36	67	2.966e-02
GO:BP	GO:0061668	mitochondrial ribosome assembly	10	13	2.997e-02
GO:BP	GO:0006054	N-acetylneuraminate metabolic process	10	13	2.997e-02
GO:BP	GO:0009304	tRNA transcription	10	13	2.997e-02
GO:BP	GO:0006264	mitochondrial DNA replication	10	13	2.997e-02
GO:BP	GO:0061795	Golgi lumen acidification	10	13	2.997e-02
GO:BP	GO:0010992	ubiquitin recycling	10	13	2.997e-02
GO:BP	GO:0034982	mitochondrial protein processing	10	13	2.997e-02
GO:BP	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	10	13	2.997e-02
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	54	108	3.032e-02
GO:BP	GO:0045089	positive regulation of innate immune response	164	374	3.063e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	57	115	3.063e-02
GO:BP	GO:0043473	pigmentation	57	115	3.063e-02
GO:BP	GO:0038127	ERBB signaling pathway	63	129	3.064e-02
GO:BP	GO:0001952	regulation of cell-matrix adhesion	60	122	3.070e-02
GO:BP	GO:0051046	regulation of secretion	261	617	3.070e-02
GO:BP	GO:0033260	nuclear DNA replication	24	41	3.078e-02
GO:BP	GO:1902305	regulation of sodium ion transmembrane transport	24	41	3.078e-02
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	24	41	3.078e-02
GO:BP	GO:2000008	regulation of protein localization to cell surface	24	41	3.078e-02
GO:BP	GO:0072210	metanephric nephron development	24	41	3.078e-02
GO:BP	GO:0045738	negative regulation of DNA repair	24	41	3.078e-02
GO:BP	GO:0009791	post-embryonic development	47	92	3.086e-02
GO:BP	GO:0034605	cellular response to heat	35	65	3.149e-02
GO:BP	GO:0050771	negative regulation of axonogenesis	30	54	3.161e-02
GO:BP	GO:1905039	carboxylic acid transmembrane transport	71	148	3.161e-02
GO:BP	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	30	54	3.161e-02
GO:BP	GO:0046605	regulation of centrosome cycle	30	54	3.161e-02
GO:BP	GO:0061333	renal tubule morphogenesis	43	83	3.170e-02
GO:BP	GO:0043648	dicarboxylic acid metabolic process	50	99	3.174e-02
GO:BP	GO:0007616	long-term memory	23	39	3.225e-02
GO:BP	GO:0035264	multicellular organism growth	76	160	3.247e-02
GO:BP	GO:0034284	response to monosaccharide	101	220	3.255e-02
GO:BP	GO:0062207	regulation of pattern recognition receptor signaling pathway	81	172	3.299e-02
GO:BP	GO:0048592	eye morphogenesis	81	172	3.299e-02
GO:BP	GO:0006790	sulfur compound metabolic process	137	308	3.307e-02
GO:BP	GO:0010171	body morphogenesis	29	52	3.356e-02
GO:BP	GO:0031648	protein destabilization	29	52	3.356e-02
GO:BP	GO:0090109	regulation of cell-substrate junction assembly	34	63	3.356e-02
GO:BP	GO:0042255	ribosome assembly	34	63	3.356e-02
GO:BP	GO:0051893	regulation of focal adhesion assembly	34	63	3.356e-02
GO:BP	GO:0010001	glial cell differentiation	119	264	3.359e-02
GO:BP	GO:0031076	embryonic camera-type eye development	22	37	3.363e-02
GO:BP	GO:0060972	left/right pattern formation	70	146	3.374e-02
GO:BP	GO:0090737	telomere maintenance via telomere trimming	11	15	3.376e-02
GO:BP	GO:0090656	t-circle formation	11	15	3.376e-02
GO:BP	GO:0090306	meiotic spindle assembly	11	15	3.376e-02
GO:BP	GO:0008298	intracellular mRNA localization	11	15	3.376e-02
GO:BP	GO:0086069	bundle of His cell to Purkinje myocyte communication	11	15	3.376e-02
GO:BP	GO:0046831	regulation of RNA export from nucleus	11	15	3.376e-02
GO:BP	GO:0140042	lipid droplet formation	11	15	3.376e-02
GO:BP	GO:0050708	regulation of protein secretion	121	269	3.376e-02
GO:BP	GO:0033750	ribosome localization	11	15	3.376e-02
GO:BP	GO:0043248	proteasome assembly	11	15	3.376e-02
GO:BP	GO:0072088	nephron epithelium morphogenesis	42	81	3.376e-02
GO:BP	GO:0060211	regulation of nuclear-transcribed mRNA poly(A) tail shortening	11	15	3.376e-02
GO:BP	GO:0070986	left/right axis specification	11	15	3.376e-02
GO:BP	GO:0071027	nuclear RNA surveillance	11	15	3.376e-02
GO:BP	GO:0060413	atrial septum morphogenesis	11	15	3.376e-02
GO:BP	GO:0000054	ribosomal subunit export from nucleus	11	15	3.376e-02
GO:BP	GO:0055012	ventricular cardiac muscle cell differentiation	11	15	3.376e-02
GO:BP	GO:0001325	formation of extrachromosomal circular DNA	11	15	3.376e-02
GO:BP	GO:0070243	regulation of thymocyte apoptotic process	11	15	3.376e-02
GO:BP	GO:0007610	behavior	283	674	3.387e-02
GO:BP	GO:0008585	female gonad development	52	104	3.434e-02
GO:BP	GO:1902410	mitotic cytokinetic process	21	35	3.474e-02
GO:BP	GO:0090162	establishment of epithelial cell polarity	21	35	3.474e-02
GO:BP	GO:0060350	endochondral bone morphogenesis	33	61	3.552e-02
GO:BP	GO:0042306	regulation of protein import into nucleus	33	61	3.552e-02
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	33	61	3.552e-02
GO:BP	GO:0071692	protein localization to extracellular region	169	388	3.608e-02
GO:BP	GO:0009123	nucleoside monophosphate metabolic process	41	79	3.609e-02
GO:BP	GO:1904354	negative regulation of telomere capping	7	8	3.613e-02
GO:BP	GO:0061511	centriole elongation	7	8	3.613e-02
GO:BP	GO:0007172	signal complex assembly	7	8	3.613e-02
GO:BP	GO:0003149	membranous septum morphogenesis	7	8	3.613e-02
GO:BP	GO:0060509	type I pneumocyte differentiation	7	8	3.613e-02
GO:BP	GO:0006384	transcription initiation at RNA polymerase III promoter	7	8	3.613e-02
GO:BP	GO:0006290	pyrimidine dimer repair	7	8	3.613e-02
GO:BP	GO:0071499	cellular response to laminar fluid shear stress	7	8	3.613e-02
GO:BP	GO:2000973	regulation of pro-B cell differentiation	7	8	3.613e-02
GO:BP	GO:0003344	pericardium morphogenesis	7	8	3.613e-02
GO:BP	GO:0003211	cardiac ventricle formation	7	8	3.613e-02
GO:BP	GO:0072033	renal vesicle formation	7	8	3.613e-02
GO:BP	GO:0051086	chaperone mediated protein folding independent of cofactor	7	8	3.613e-02
GO:BP	GO:0071051	poly(A)-dependent snoRNA 3’-end processing	7	8	3.613e-02
GO:BP	GO:0034475	U4 snRNA 3’-end processing	7	8	3.613e-02
GO:BP	GO:0015959	diadenosine polyphosphate metabolic process	7	8	3.613e-02
GO:BP	GO:0150012	positive regulation of neuron projection arborization	7	8	3.613e-02
GO:BP	GO:0031077	post-embryonic camera-type eye development	7	8	3.613e-02
GO:BP	GO:0018202	peptidyl-histidine modification	7	8	3.613e-02
GO:BP	GO:0043117	positive regulation of vascular permeability	12	17	3.631e-02
GO:BP	GO:0090205	positive regulation of cholesterol metabolic process	12	17	3.631e-02
GO:BP	GO:0046653	tetrahydrofolate metabolic process	12	17	3.631e-02
GO:BP	GO:0006991	response to sterol depletion	12	17	3.631e-02
GO:BP	GO:0002098	tRNA wobble uridine modification	12	17	3.631e-02
GO:BP	GO:0033993	response to lipid	383	930	3.631e-02
GO:BP	GO:0072077	renal vesicle morphogenesis	12	17	3.631e-02
GO:BP	GO:0019218	regulation of steroid metabolic process	51	102	3.641e-02
GO:BP	GO:0072080	nephron tubule development	51	102	3.641e-02
GO:BP	GO:0051085	chaperone cofactor-dependent protein refolding	19	31	3.683e-02
GO:BP	GO:0016226	iron-sulfur cluster assembly	19	31	3.683e-02
GO:BP	GO:0070498	interleukin-1-mediated signaling pathway	19	31	3.683e-02
GO:BP	GO:0031163	metallo-sulfur cluster assembly	19	31	3.683e-02
GO:BP	GO:0045747	positive regulation of Notch signaling pathway	27	48	3.699e-02
GO:BP	GO:0044042	glucan metabolic process	44	86	3.719e-02
GO:BP	GO:0070935	3’-UTR-mediated mRNA stabilization	18	29	3.786e-02
GO:BP	GO:0034315	regulation of Arp2/3 complex-mediated actin nucleation	18	29	3.786e-02
GO:BP	GO:0090311	regulation of protein deacetylation	18	29	3.786e-02
GO:BP	GO:0099625	ventricular cardiac muscle cell membrane repolarization	18	29	3.786e-02
GO:BP	GO:0051156	glucose 6-phosphate metabolic process	18	29	3.786e-02
GO:BP	GO:0071025	RNA surveillance	13	19	3.797e-02
GO:BP	GO:0006491	N-glycan processing	13	19	3.797e-02
GO:BP	GO:1902004	positive regulation of amyloid-beta formation	13	19	3.797e-02
GO:BP	GO:0034244	negative regulation of transcription elongation by RNA polymerase II	13	19	3.797e-02
GO:BP	GO:0035372	protein localization to microtubule	13	19	3.797e-02
GO:BP	GO:0009084	glutamine family amino acid biosynthetic process	13	19	3.797e-02
GO:BP	GO:1903533	regulation of protein targeting	40	77	3.803e-02
GO:BP	GO:0070373	negative regulation of ERK1 and ERK2 cascade	36	68	3.823e-02
GO:BP	GO:1901605	alpha-amino acid metabolic process	98	214	3.824e-02
GO:BP	GO:0009226	nucleotide-sugar biosynthetic process	17	27	3.851e-02
GO:BP	GO:0051043	regulation of membrane protein ectodomain proteolysis	17	27	3.851e-02
GO:BP	GO:0031468	nuclear membrane reassembly	17	27	3.851e-02
GO:BP	GO:0060544	regulation of necroptotic process	17	27	3.851e-02
GO:BP	GO:0016188	synaptic vesicle maturation	17	27	3.851e-02
GO:BP	GO:0006450	regulation of translational fidelity	14	21	3.873e-02
GO:BP	GO:0016556	mRNA modification	14	21	3.873e-02
GO:BP	GO:0072663	establishment of protein localization to peroxisome	14	21	3.873e-02
GO:BP	GO:0072662	protein localization to peroxisome	14	21	3.873e-02
GO:BP	GO:0071474	cellular hyperosmotic response	14	21	3.873e-02
GO:BP	GO:0006029	proteoglycan metabolic process	50	100	3.873e-02
GO:BP	GO:0140896	cGAS/STING signaling pathway	14	21	3.873e-02
GO:BP	GO:0071229	cellular response to acid chemical	50	100	3.873e-02
GO:BP	GO:0090043	regulation of tubulin deacetylation	14	21	3.873e-02
GO:BP	GO:0002183	cytoplasmic translational initiation	26	46	3.882e-02
GO:BP	GO:0007020	microtubule nucleation	26	46	3.882e-02
GO:BP	GO:1903241	U2-type prespliceosome assembly	16	25	3.887e-02
GO:BP	GO:1901983	regulation of protein acetylation	15	23	3.891e-02
GO:BP	GO:1905709	negative regulation of membrane permeability	15	23	3.891e-02
GO:BP	GO:0090042	tubulin deacetylation	15	23	3.891e-02
GO:BP	GO:0140112	extracellular vesicle biogenesis	15	23	3.891e-02
GO:BP	GO:0006672	ceramide metabolic process	53	107	3.891e-02
GO:BP	GO:0051904	pigment granule transport	15	23	3.891e-02
GO:BP	GO:0035331	negative regulation of hippo signaling	15	23	3.891e-02
GO:BP	GO:0031098	stress-activated protein kinase signaling cascade	31	57	3.942e-02
GO:BP	GO:0050435	amyloid-beta metabolic process	31	57	3.942e-02
GO:BP	GO:0003170	heart valve development	39	75	4.045e-02
GO:BP	GO:0042157	lipoprotein metabolic process	46	91	4.053e-02
GO:BP	GO:0006767	water-soluble vitamin metabolic process	35	66	4.053e-02
GO:BP	GO:0006903	vesicle targeting	35	66	4.053e-02
GO:BP	GO:0051492	regulation of stress fiber assembly	46	91	4.053e-02
GO:BP	GO:1901879	regulation of protein depolymerization	46	91	4.053e-02
GO:BP	GO:0070301	cellular response to hydrogen peroxide	35	66	4.053e-02
GO:BP	GO:0001890	placenta development	72	152	4.092e-02
GO:BP	GO:0048701	embryonic cranial skeleton morphogenesis	25	44	4.093e-02
GO:BP	GO:0009225	nucleotide-sugar metabolic process	25	44	4.093e-02
GO:BP	GO:0042542	response to hydrogen peroxide	49	98	4.128e-02
GO:BP	GO:0008203	cholesterol metabolic process	69	145	4.192e-02
GO:BP	GO:0002042	cell migration involved in sprouting angiogenesis	30	55	4.205e-02
GO:BP	GO:0038066	p38MAPK cascade	30	55	4.205e-02
GO:BP	GO:0010657	muscle cell apoptotic process	42	82	4.221e-02
GO:BP	GO:0006814	sodium ion transport	110	244	4.243e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	66	138	4.276e-02
GO:BP	GO:0003158	endothelium development	66	138	4.276e-02
GO:BP	GO:0010662	regulation of striated muscle cell apoptotic process	24	42	4.334e-02
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	24	42	4.334e-02
GO:BP	GO:0099068	postsynapse assembly	45	89	4.350e-02
GO:BP	GO:0006631	fatty acid metabolic process	173	400	4.357e-02
GO:BP	GO:1903706	regulation of hemopoiesis	183	425	4.358e-02
GO:BP	GO:0050714	positive regulation of protein secretion	71	150	4.371e-02
GO:BP	GO:0006090	pyruvate metabolic process	60	124	4.414e-02
GO:BP	GO:0045639	positive regulation of myeloid cell differentiation	51	103	4.474e-02
GO:BP	GO:0045912	negative regulation of carbohydrate metabolic process	29	53	4.480e-02
GO:BP	GO:0170034	L-amino acid biosynthetic process	29	53	4.480e-02
GO:BP	GO:0010596	negative regulation of endothelial cell migration	29	53	4.480e-02
GO:BP	GO:2001222	regulation of neuron migration	29	53	4.480e-02
GO:BP	GO:0070987	error-free translesion synthesis	5	5	4.572e-02
GO:BP	GO:1901908	diadenosine hexaphosphate metabolic process	5	5	4.572e-02
GO:BP	GO:1901910	adenosine 5’-(hexahydrogen pentaphosphate) metabolic process	5	5	4.572e-02
GO:BP	GO:1903724	positive regulation of centriole elongation	5	5	4.572e-02
GO:BP	GO:0071543	diphosphoinositol polyphosphate metabolic process	5	5	4.572e-02
GO:BP	GO:1901909	diadenosine hexaphosphate catabolic process	5	5	4.572e-02
GO:BP	GO:1901907	diadenosine pentaphosphate catabolic process	5	5	4.572e-02
GO:BP	GO:0061431	cellular response to methionine	5	5	4.572e-02
GO:BP	GO:1901911	adenosine 5’-(hexahydrogen pentaphosphate) catabolic process	5	5	4.572e-02
GO:BP	GO:0060922	atrioventricular node cell differentiation	5	5	4.572e-02
GO:BP	GO:0019042	viral latency	5	5	4.572e-02
GO:BP	GO:0048790	maintenance of presynaptic active zone structure	5	5	4.572e-02
GO:BP	GO:0090199	regulation of release of cytochrome c from mitochondria	23	40	4.572e-02
GO:BP	GO:0098708	D-glucose import across plasma membrane	5	5	4.572e-02
GO:BP	GO:0042350	GDP-L-fucose biosynthetic process	5	5	4.572e-02
GO:BP	GO:2000051	negative regulation of non-canonical Wnt signaling pathway	5	5	4.572e-02
GO:BP	GO:0086045	membrane depolarization during AV node cell action potential	5	5	4.572e-02
GO:BP	GO:1901906	diadenosine pentaphosphate metabolic process	5	5	4.572e-02
GO:BP	GO:0006297	nucleotide-excision repair, DNA gap filling	5	5	4.572e-02
GO:BP	GO:0006113	fermentation	5	5	4.572e-02
GO:BP	GO:0019509	L-methionine salvage from methylthioadenosine	5	5	4.572e-02
GO:BP	GO:0048753	pigment granule organization	23	40	4.572e-02
GO:BP	GO:1990592	protein K69-linked ufmylation	5	5	4.572e-02
GO:BP	GO:0033499	galactose catabolic process via UDP-galactose, Leloir pathway	5	5	4.572e-02
GO:BP	GO:1905908	positive regulation of amyloid fibril formation	5	5	4.572e-02
GO:BP	GO:1990564	protein polyufmylation	5	5	4.572e-02
GO:BP	GO:0003431	growth plate cartilage chondrocyte development	5	5	4.572e-02
GO:BP	GO:0018027	peptidyl-lysine dimethylation	5	5	4.572e-02
GO:BP	GO:1904978	regulation of endosome organization	5	5	4.572e-02
GO:BP	GO:0003292	cardiac septum cell differentiation	5	5	4.572e-02
GO:BP	GO:0014015	positive regulation of gliogenesis	37	71	4.577e-02
GO:BP	GO:0042058	regulation of epidermal growth factor receptor signaling pathway	33	62	4.579e-02
GO:BP	GO:0009799	specification of symmetry	70	148	4.614e-02
GO:BP	GO:0009855	determination of bilateral symmetry	70	148	4.614e-02
GO:BP	GO:0016125	sterol metabolic process	75	160	4.661e-02
GO:BP	GO:0072006	nephron development	75	160	4.661e-02
GO:BP	GO:0071482	cellular response to light stimulus	59	122	4.664e-02
GO:BP	GO:0000492	box C/D snoRNP assembly	8	10	4.695e-02
GO:BP	GO:0086016	AV node cell action potential	8	10	4.695e-02
GO:BP	GO:1904869	regulation of protein localization to Cajal body	8	10	4.695e-02
GO:BP	GO:0070862	negative regulation of protein exit from endoplasmic reticulum	8	10	4.695e-02
GO:BP	GO:0071166	ribonucleoprotein complex localization	8	10	4.695e-02
GO:BP	GO:0086027	AV node cell to bundle of His cell signaling	8	10	4.695e-02
GO:BP	GO:0060052	neurofilament cytoskeleton organization	8	10	4.695e-02
GO:BP	GO:1904871	positive regulation of protein localization to Cajal body	8	10	4.695e-02
GO:BP	GO:0006625	protein targeting to peroxisome	8	10	4.695e-02
GO:BP	GO:2000756	regulation of peptidyl-lysine acetylation	8	10	4.695e-02
GO:BP	GO:0060628	regulation of ER to Golgi vesicle-mediated transport	8	10	4.695e-02
GO:BP	GO:0071600	otic vesicle morphogenesis	8	10	4.695e-02
GO:BP	GO:2000739	regulation of mesenchymal stem cell differentiation	8	10	4.695e-02
GO:BP	GO:0046545	development of primary female sexual characteristics	53	108	4.710e-02
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	22	38	4.734e-02
GO:BP	GO:0099172	presynapse organization	32	60	4.883e-02
GO:BP	GO:0002381	immunoglobulin production involved in immunoglobulin-mediated immune response	32	60	4.883e-02
GO:BP	GO:0033014	tetrapyrrole biosynthetic process	21	36	4.989e-02
GO:BP	GO:1902745	positive regulation of lamellipodium organization	21	36	4.989e-02
GO:BP	GO:0006779	porphyrin-containing compound biosynthetic process	21	36	4.989e-02
GO:BP	GO:0007035	vacuolar acidification	21	36	4.989e-02
GO:BP	GO:0090630	activation of GTPase activity	21	36	4.989e-02
GO:BP	GO:0032885	regulation of polysaccharide biosynthetic process	21	36	4.989e-02
GO:BP	GO:1902003	regulation of amyloid-beta formation	21	36	4.989e-02
KEGG	KEGG:04140	Autophagy - animal	111	165	1.401e-07
KEGG	KEGG:05168	Herpes simplex virus 1 infection	283	506	7.029e-07
KEGG	KEGG:04137	Mitophagy - animal	72	103	5.134e-06
KEGG	KEGG:03082	ATP-dependent chromatin remodeling	75	116	2.104e-04
KEGG	KEGG:05212	Pancreatic cancer	53	76	2.104e-04
KEGG	KEGG:04070	Phosphatidylinositol signaling system	64	97	3.365e-04
KEGG	KEGG:05210	Colorectal cancer	57	86	7.571e-04
KEGG	KEGG:03018	RNA degradation	53	79	7.789e-04
KEGG	KEGG:04919	Thyroid hormone signaling pathway	75	121	1.079e-03
KEGG	KEGG:03013	Nucleocytoplasmic transport	68	108	1.100e-03
KEGG	KEGG:03083	Polycomb repressive complex	55	84	1.150e-03
KEGG	KEGG:04144	Endocytosis	138	248	1.736e-03
KEGG	KEGG:00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	21	26	2.922e-03
KEGG	KEGG:04218	Cellular senescence	90	155	2.922e-03
KEGG	KEGG:04150	mTOR signaling pathway	90	155	2.922e-03
KEGG	KEGG:05223	Non-small cell lung cancer	47	72	2.922e-03
KEGG	KEGG:05225	Hepatocellular carcinoma	96	166	2.922e-03
KEGG	KEGG:04115	p53 signaling pathway	48	74	2.922e-03
KEGG	KEGG:04110	Cell cycle	91	157	2.922e-03
KEGG	KEGG:05169	Epstein-Barr virus infection	111	198	3.600e-03
KEGG	KEGG:05161	Hepatitis B	93	162	3.600e-03
KEGG	KEGG:05131	Shigellosis	134	246	4.346e-03
KEGG	KEGG:04136	Autophagy - other	24	32	4.425e-03
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	81	140	5.404e-03
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	95	168	5.404e-03
KEGG	KEGG:05213	Endometrial cancer	38	58	7.595e-03
KEGG	KEGG:04152	AMPK signaling pathway	70	120	8.842e-03
KEGG	KEGG:00970	Aminoacyl-tRNA biosynthesis	30	44	9.952e-03
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	187	363	1.158e-02
KEGG	KEGG:03022	Basal transcription factors	29	43	1.437e-02
KEGG	KEGG:05226	Gastric cancer	83	148	1.437e-02
KEGG	KEGG:04330	Notch signaling pathway	38	60	1.615e-02
KEGG	KEGG:01522	Endocrine resistance	56	95	1.721e-02
KEGG	KEGG:04310	Wnt signaling pathway	95	174	1.891e-02
KEGG	KEGG:00513	Various types of N-glycan biosynthesis	28	42	2.015e-02
KEGG	KEGG:03410	Base excision repair	29	44	2.133e-02
KEGG	KEGG:03420	Nucleotide excision repair	38	61	2.166e-02
KEGG	KEGG:04010	MAPK signaling pathway	155	301	2.379e-02
KEGG	KEGG:05224	Breast cancer	81	147	2.470e-02
KEGG	KEGG:05017	Spinocerebellar ataxia	78	141	2.481e-02
KEGG	KEGG:04211	Longevity regulating pathway	52	89	2.545e-02
KEGG	KEGG:05203	Viral carcinogenesis	107	201	2.545e-02
KEGG	KEGG:04350	TGF-beta signaling pathway	61	107	2.550e-02
KEGG	KEGG:04360	Axon guidance	97	181	2.819e-02
KEGG	KEGG:04710	Circadian rhythm	23	34	2.895e-02
KEGG	KEGG:03020	RNA polymerase	23	34	2.895e-02
KEGG	KEGG:04390	Hippo signaling pathway	85	157	3.092e-02
KEGG	KEGG:04931	Insulin resistance	61	108	3.092e-02
KEGG	KEGG:00510	N-Glycan biosynthesis	33	53	3.157e-02
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	114	218	3.385e-02
KEGG	KEGG:00310	Lysine degradation	38	63	3.509e-02
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	46	79	3.808e-02
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	233	474	3.822e-02
KEGG	KEGG:04071	Sphingolipid signaling pathway	66	120	4.455e-02
KEGG	KEGG:04012	ErbB signaling pathway	48	84	4.849e-02
KEGG	KEGG:03440	Homologous recombination	26	41	4.849e-02
KEGG	KEGG:04910	Insulin signaling pathway	74	137	4.849e-02

#GO:BP
table_DOX24Tshare_genes_GOBP <- table_DOX24Tshare_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24Tshare_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24Tshare_genes_KEGG <- table_DOX24Tshare_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24Tshare_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX24R DEGs GO KEGG#####
D24R_DEGs_mat <- as.matrix(DOX24R_DEGs_GO)

DOX_24R_dxr_gene <- gost(query = D24R_DEGs_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24R_gost_genes <- gostplot(DOX_24R_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24R_gost_genes

table_DOX24R_genes <- DOX_24R_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24R_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0007275	multicellular organism development	578	4727	1.297e-16
GO:BP	GO:0032502	developmental process	754	6553	1.297e-16
GO:BP	GO:0048856	anatomical structure development	699	5997	2.247e-16
GO:BP	GO:0048731	system development	507	4053	4.867e-16
GO:BP	GO:0006810	transport	526	4407	8.570e-13
GO:BP	GO:0051179	localization	637	5555	8.570e-13
GO:BP	GO:0032501	multicellular organismal process	798	7322	4.356e-12
GO:BP	GO:0006996	organelle organization	440	3594	7.388e-12
GO:BP	GO:0048518	positive regulation of biological process	697	6264	1.037e-11
GO:BP	GO:0006796	phosphate-containing compound metabolic process	316	2407	1.931e-11
GO:BP	GO:0006793	phosphorus metabolic process	316	2410	2.074e-11
GO:BP	GO:0048522	positive regulation of cellular process	661	5920	3.346e-11
GO:BP	GO:0010646	regulation of cell communication	424	3486	4.996e-11
GO:BP	GO:0030029	actin filament-based process	137	825	9.458e-11
GO:BP	GO:0007010	cytoskeleton organization	218	1529	9.520e-11
GO:BP	GO:0023051	regulation of signaling	421	3478	1.099e-10
GO:BP	GO:0051234	establishment of localization	562	4928	1.506e-10
GO:BP	GO:0065007	biological regulation	1262	12743	1.745e-10
GO:BP	GO:0007399	nervous system development	330	2604	2.769e-10
GO:BP	GO:0030036	actin cytoskeleton organization	123	729	4.020e-10
GO:BP	GO:0048513	animal organ development	377	3085	6.485e-10
GO:BP	GO:0033554	cellular response to stress	246	1830	9.967e-10
GO:BP	GO:0030154	cell differentiation	509	4437	1.062e-09
GO:BP	GO:0048869	cellular developmental process	509	4438	1.062e-09
GO:BP	GO:0019538	protein metabolic process	535	4721	1.682e-09
GO:BP	GO:0003012	muscle system process	84	438	1.846e-09
GO:BP	GO:0051641	cellular localization	431	3661	2.218e-09
GO:BP	GO:0051239	regulation of multicellular organismal process	360	2956	2.903e-09
GO:BP	GO:0050789	regulation of biological process	1218	12336	3.289e-09
GO:BP	GO:0009653	anatomical structure morphogenesis	335	2713	3.289e-09
GO:BP	GO:0048583	regulation of response to stimulus	462	3993	3.652e-09
GO:BP	GO:0016192	vesicle-mediated transport	217	1592	4.401e-09
GO:BP	GO:0097435	supramolecular fiber organization	134	861	8.667e-09
GO:BP	GO:0065008	regulation of biological quality	356	2947	9.267e-09
GO:BP	GO:0044281	small molecule metabolic process	235	1776	1.019e-08
GO:BP	GO:0050896	response to stimulus	922	8999	1.620e-08
GO:BP	GO:0009966	regulation of signal transduction	363	3034	1.777e-08
GO:BP	GO:0030334	regulation of cell migration	144	960	2.026e-08
GO:BP	GO:0051716	cellular response to stimulus	774	7376	2.560e-08
GO:BP	GO:0061061	muscle structure development	112	693	3.261e-08
GO:BP	GO:0016477	cell migration	206	1534	4.542e-08
GO:BP	GO:0006936	muscle contraction	68	349	5.944e-08
GO:BP	GO:0072359	circulatory system development	162	1145	1.046e-07
GO:BP	GO:2000145	regulation of cell motility	148	1022	1.201e-07
GO:BP	GO:0032879	regulation of localization	256	2029	1.224e-07
GO:BP	GO:0022008	neurogenesis	229	1771	1.240e-07
GO:BP	GO:0044057	regulation of system process	93	553	1.304e-07
GO:BP	GO:0048519	negative regulation of biological process	625	5834	1.893e-07
GO:BP	GO:0048870	cell motility	230	1793	2.124e-07
GO:BP	GO:0006091	generation of precursor metabolites and energy	83	478	2.124e-07
GO:BP	GO:0030030	cell projection organization	213	1631	2.124e-07
GO:BP	GO:0036211	protein modification process	337	2846	2.478e-07
GO:BP	GO:0040012	regulation of locomotion	151	1067	3.363e-07
GO:BP	GO:0051128	regulation of cellular component organization	294	2433	4.468e-07
GO:BP	GO:0043412	macromolecule modification	353	3030	5.741e-07
GO:BP	GO:0046907	intracellular transport	184	1381	6.118e-07
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	206	1588	6.118e-07
GO:BP	GO:0051649	establishment of localization in cell	250	2010	6.118e-07
GO:BP	GO:0090257	regulation of muscle system process	49	231	7.325e-07
GO:BP	GO:0040007	growth	134	929	7.664e-07
GO:BP	GO:0007015	actin filament organization	79	461	8.199e-07
GO:BP	GO:0050794	regulation of cellular process	1164	11946	1.124e-06
GO:BP	GO:0048523	negative regulation of cellular process	599	5629	1.269e-06
GO:BP	GO:0009056	catabolic process	311	2639	1.686e-06
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	63	345	2.366e-06
GO:BP	GO:0009060	aerobic respiration	43	199	3.172e-06
GO:BP	GO:0040011	locomotion	167	1255	3.179e-06
GO:BP	GO:0007155	cell adhesion	196	1530	3.375e-06
GO:BP	GO:0023057	negative regulation of signaling	186	1435	3.375e-06
GO:BP	GO:0048585	negative regulation of response to stimulus	211	1680	4.469e-06
GO:BP	GO:0019637	organophosphate metabolic process	147	1077	4.469e-06
GO:BP	GO:0009888	tissue development	247	2032	4.696e-06
GO:BP	GO:0034330	cell junction organization	120	834	4.696e-06
GO:BP	GO:0010648	negative regulation of cell communication	185	1436	5.349e-06
GO:BP	GO:0090407	organophosphate biosynthetic process	95	619	5.970e-06
GO:BP	GO:0050793	regulation of developmental process	289	2457	6.304e-06
GO:BP	GO:0031175	neuron projection development	140	1023	7.533e-06
GO:BP	GO:0006937	regulation of muscle contraction	37	165	9.132e-06
GO:BP	GO:0051246	regulation of protein metabolic process	227	1855	9.763e-06
GO:BP	GO:0006950	response to stress	433	3948	9.928e-06
GO:BP	GO:0007507	heart development	92	605	1.384e-05
GO:BP	GO:0031344	regulation of cell projection organization	98	658	1.472e-05
GO:BP	GO:0048699	generation of neurons	193	1536	1.503e-05
GO:BP	GO:0007154	cell communication	673	6540	1.768e-05
GO:BP	GO:0045333	cellular respiration	47	242	1.768e-05
GO:BP	GO:0030335	positive regulation of cell migration	86	559	1.995e-05
GO:BP	GO:0048589	developmental growth	98	663	1.995e-05
GO:BP	GO:0040017	positive regulation of locomotion	91	603	2.113e-05
GO:BP	GO:0005975	carbohydrate metabolic process	86	561	2.268e-05
GO:BP	GO:0030182	neuron differentiation	183	1451	2.331e-05
GO:BP	GO:0070727	cellular macromolecule localization	317	2782	2.446e-05
GO:BP	GO:0051049	regulation of transport	199	1607	2.471e-05
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	95	642	2.727e-05
GO:BP	GO:0033036	macromolecule localization	360	3228	2.802e-05
GO:BP	GO:0043603	amide metabolic process	73	455	2.973e-05
GO:BP	GO:0008104	protein localization	315	2770	3.090e-05
GO:BP	GO:0023052	signaling	668	6515	3.195e-05
GO:BP	GO:0019752	carboxylic acid metabolic process	122	887	3.254e-05
GO:BP	GO:0080090	regulation of primary metabolic process	564	5390	3.369e-05
GO:BP	GO:0009611	response to wounding	86	568	3.469e-05
GO:BP	GO:0048666	neuron development	153	1177	3.612e-05
GO:BP	GO:0007166	cell surface receptor signaling pathway	319	2819	3.824e-05
GO:BP	GO:2000147	positive regulation of cell motility	88	587	3.824e-05
GO:BP	GO:0044087	regulation of cellular component biogenesis	135	1011	3.959e-05
GO:BP	GO:0065009	regulation of molecular function	186	1496	4.215e-05
GO:BP	GO:0060047	heart contraction	46	244	4.649e-05
GO:BP	GO:0006082	organic acid metabolic process	124	915	5.275e-05
GO:BP	GO:0043436	oxoacid metabolic process	123	909	6.284e-05
GO:BP	GO:0006812	monoatomic cation transport	140	1069	6.988e-05
GO:BP	GO:0009719	response to endogenous stimulus	184	1489	6.999e-05
GO:BP	GO:0006979	response to oxidative stress	65	400	7.047e-05
GO:BP	GO:0043500	muscle adaptation	26	105	7.070e-05
GO:BP	GO:0055085	transmembrane transport	193	1578	7.285e-05
GO:BP	GO:0061564	axon development	80	528	7.469e-05
GO:BP	GO:0016310	phosphorylation	166	1320	8.230e-05
GO:BP	GO:0006468	protein phosphorylation	156	1227	9.231e-05
GO:BP	GO:0009893	positive regulation of metabolic process	391	3597	9.349e-05
GO:BP	GO:0035556	intracellular signal transduction	330	2965	9.695e-05
GO:BP	GO:0031589	cell-substrate adhesion	59	356	1.081e-04
GO:BP	GO:0003015	heart process	46	253	1.176e-04
GO:BP	GO:0098655	monoatomic cation transmembrane transport	118	877	1.251e-04
GO:BP	GO:0050808	synapse organization	83	563	1.350e-04
GO:BP	GO:0098660	inorganic ion transmembrane transport	125	944	1.386e-04
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	87	599	1.407e-04
GO:BP	GO:0034220	monoatomic ion transmembrane transport	136	1048	1.440e-04
GO:BP	GO:0030198	extracellular matrix organization	55	327	1.441e-04
GO:BP	GO:0009968	negative regulation of signal transduction	165	1326	1.528e-04
GO:BP	GO:0043062	extracellular structure organization	55	328	1.561e-04
GO:BP	GO:0045229	external encapsulating structure organization	55	329	1.704e-04
GO:BP	GO:0006811	monoatomic ion transport	160	1282	1.803e-04
GO:BP	GO:0090066	regulation of anatomical structure size	75	500	2.052e-04
GO:BP	GO:0032535	regulation of cellular component size	58	356	2.072e-04
GO:BP	GO:0051240	positive regulation of multicellular organismal process	199	1667	2.147e-04
GO:BP	GO:1901135	carbohydrate derivative metabolic process	128	983	2.271e-04
GO:BP	GO:0042060	wound healing	67	433	2.283e-04
GO:BP	GO:0062197	cellular response to chemical stress	53	317	2.434e-04
GO:BP	GO:0032970	regulation of actin filament-based process	60	376	2.682e-04
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	94	673	2.687e-04
GO:BP	GO:0044283	small molecule biosynthetic process	85	593	2.781e-04
GO:BP	GO:0043069	negative regulation of programmed cell death	119	905	3.018e-04
GO:BP	GO:0010975	regulation of neuron projection development	68	446	3.104e-04
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	51	304	3.168e-04
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	51	304	3.168e-04
GO:BP	GO:0015031	protein transport	175	1444	3.330e-04
GO:BP	GO:0030239	myofibril assembly	20	76	3.570e-04
GO:BP	GO:0019725	cellular homeostasis	111	835	3.680e-04
GO:BP	GO:0060314	regulation of ryanodine-sensitive calcium-release channel activity	10	22	3.763e-04
GO:BP	GO:0000902	cell morphogenesis	128	996	3.972e-04
GO:BP	GO:0098657	import into cell	120	922	4.229e-04
GO:BP	GO:0006753	nucleoside phosphate metabolic process	90	646	4.363e-04
GO:BP	GO:0006790	sulfur compound metabolic process	51	308	4.379e-04
GO:BP	GO:0055001	muscle cell development	37	198	4.915e-04
GO:BP	GO:0006119	oxidative phosphorylation	30	146	4.973e-04
GO:BP	GO:0001933	negative regulation of protein phosphorylation	43	245	4.993e-04
GO:BP	GO:0007165	signal transduction	608	6002	5.230e-04
GO:BP	GO:0007409	axonogenesis	69	463	5.273e-04
GO:BP	GO:0012501	programmed cell death	228	1987	5.510e-04
GO:BP	GO:0042592	homeostatic process	203	1736	5.510e-04
GO:BP	GO:0001706	endoderm formation	17	60	5.510e-04
GO:BP	GO:0051051	negative regulation of transport	63	412	5.510e-04
GO:BP	GO:0097190	apoptotic signaling pathway	85	606	5.579e-04
GO:BP	GO:0098662	inorganic cation transmembrane transport	112	854	5.579e-04
GO:BP	GO:0048878	chemical homeostasis	132	1043	5.588e-04
GO:BP	GO:0008015	blood circulation	75	518	5.939e-04
GO:BP	GO:0008219	cell death	228	1991	6.111e-04
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	148	1199	6.111e-04
GO:BP	GO:0048858	cell projection morphogenesis	93	681	6.261e-04
GO:BP	GO:0055002	striated muscle cell development	33	171	6.677e-04
GO:BP	GO:0048468	cell development	314	2876	6.705e-04
GO:BP	GO:0003013	circulatory system process	84	602	7.249e-04
GO:BP	GO:0071495	cellular response to endogenous stimulus	150	1223	7.255e-04
GO:BP	GO:0016311	dephosphorylation	39	218	7.277e-04
GO:BP	GO:0019318	hexose metabolic process	40	226	7.343e-04
GO:BP	GO:0005996	monosaccharide metabolic process	43	250	7.406e-04
GO:BP	GO:0030336	negative regulation of cell migration	48	292	8.406e-04
GO:BP	GO:0001704	formation of primary germ layer	27	129	8.408e-04
GO:BP	GO:0031032	actomyosin structure organization	38	212	8.652e-04
GO:BP	GO:0042326	negative regulation of phosphorylation	44	260	8.785e-04
GO:BP	GO:0006941	striated muscle contraction	35	189	8.830e-04
GO:BP	GO:0042063	gliogenesis	55	352	9.346e-04
GO:BP	GO:0035987	endodermal cell differentiation	15	51	9.743e-04
GO:BP	GO:0060074	synapse maturation	13	40	1.048e-03
GO:BP	GO:0042692	muscle cell differentiation	61	405	1.048e-03
GO:BP	GO:0060341	regulation of cellular localization	127	1013	1.124e-03
GO:BP	GO:0006974	DNA damage response	116	908	1.124e-03
GO:BP	GO:0110053	regulation of actin filament organization	44	263	1.124e-03
GO:BP	GO:0019220	regulation of phosphate metabolic process	121	956	1.134e-03
GO:BP	GO:0006915	apoptotic process	219	1923	1.166e-03
GO:BP	GO:0051174	regulation of phosphorus metabolic process	121	957	1.176e-03
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	91	676	1.189e-03
GO:BP	GO:0031102	neuron projection regeneration	16	58	1.200e-03
GO:BP	GO:0051248	negative regulation of protein metabolic process	91	677	1.245e-03
GO:BP	GO:0099003	vesicle-mediated transport in synapse	43	257	1.316e-03
GO:BP	GO:0048729	tissue morphogenesis	84	614	1.316e-03
GO:BP	GO:0070887	cellular response to chemical stimulus	245	2192	1.316e-03
GO:BP	GO:0001944	vasculature development	100	762	1.321e-03
GO:BP	GO:0048812	neuron projection morphogenesis	89	660	1.321e-03
GO:BP	GO:0051050	positive regulation of transport	109	847	1.351e-03
GO:BP	GO:2000146	negative regulation of cell motility	49	308	1.464e-03
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	52	334	1.545e-03
GO:BP	GO:0072521	purine-containing compound metabolic process	78	563	1.572e-03
GO:BP	GO:0040013	negative regulation of locomotion	51	326	1.590e-03
GO:BP	GO:0043502	regulation of muscle adaptation	19	79	1.714e-03
GO:BP	GO:0008016	regulation of heart contraction	36	204	1.737e-03
GO:BP	GO:0085029	extracellular matrix assembly	14	48	1.791e-03
GO:BP	GO:0009057	macromolecule catabolic process	167	1417	1.801e-03
GO:BP	GO:0016049	cell growth	69	485	1.834e-03
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	121	970	1.951e-03
GO:BP	GO:0031399	regulation of protein modification process	129	1049	2.114e-03
GO:BP	GO:0071363	cellular response to growth factor stimulus	91	689	2.205e-03
GO:BP	GO:0007517	muscle organ development	55	365	2.213e-03
GO:BP	GO:0034599	cellular response to oxidative stress	41	247	2.213e-03
GO:BP	GO:0051282	regulation of sequestering of calcium ion	26	130	2.241e-03
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	106	831	2.296e-03
GO:BP	GO:0031400	negative regulation of protein modification process	53	349	2.399e-03
GO:BP	GO:0031345	negative regulation of cell projection organization	33	184	2.404e-03
GO:BP	GO:0045595	regulation of cell differentiation	182	1576	2.404e-03
GO:BP	GO:0043067	regulation of programmed cell death	175	1506	2.404e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	95	730	2.553e-03
GO:BP	GO:0008347	glial cell migration	16	62	2.553e-03
GO:BP	GO:0070848	response to growth factor	94	721	2.590e-03
GO:BP	GO:0030534	adult behavior	29	154	2.621e-03
GO:BP	GO:0071705	nitrogen compound transport	216	1923	2.636e-03
GO:BP	GO:0080135	regulation of cellular response to stress	72	519	2.654e-03
GO:BP	GO:0060315	negative regulation of ryanodine-sensitive calcium-release channel activity	6	10	2.682e-03
GO:BP	GO:0030199	collagen fibril organization	17	69	2.789e-03
GO:BP	GO:0006886	intracellular protein transport	90	686	2.854e-03
GO:BP	GO:0048588	developmental cell growth	38	226	2.854e-03
GO:BP	GO:0031099	regeneration	35	202	2.889e-03
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	80	594	2.916e-03
GO:BP	GO:0034329	cell junction assembly	70	503	2.925e-03
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	44	276	2.935e-03
GO:BP	GO:0040008	regulation of growth	81	604	3.010e-03
GO:BP	GO:0006942	regulation of striated muscle contraction	21	97	3.153e-03
GO:BP	GO:0010811	positive regulation of cell-substrate adhesion	25	126	3.206e-03
GO:BP	GO:0048193	Golgi vesicle transport	48	312	3.366e-03
GO:BP	GO:0030155	regulation of cell adhesion	101	794	3.366e-03
GO:BP	GO:1903224	regulation of endodermal cell differentiation	5	7	3.366e-03
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	41	253	3.366e-03
GO:BP	GO:0006897	endocytosis	92	709	3.366e-03
GO:BP	GO:0051208	sequestering of calcium ion	26	134	3.366e-03
GO:BP	GO:0032787	monocarboxylic acid metabolic process	82	616	3.366e-03
GO:BP	GO:2000026	regulation of multicellular organismal development	165	1418	3.366e-03
GO:BP	GO:0060048	cardiac muscle contraction	27	142	3.514e-03
GO:BP	GO:0051209	release of sequestered calcium ion into cytosol	25	127	3.514e-03
GO:BP	GO:0019646	aerobic electron transport chain	20	91	3.514e-03
GO:BP	GO:0044092	negative regulation of molecular function	75	553	3.591e-03
GO:BP	GO:0045184	establishment of protein localization	216	1937	3.659e-03
GO:BP	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	23	113	3.795e-03
GO:BP	GO:0048675	axon extension	23	113	3.795e-03
GO:BP	GO:0006749	glutathione metabolic process	14	52	3.840e-03
GO:BP	GO:0051283	negative regulation of sequestering of calcium ion	25	128	3.885e-03
GO:BP	GO:0044093	positive regulation of molecular function	110	884	3.885e-03
GO:BP	GO:1902600	proton transmembrane transport	33	190	3.924e-03
GO:BP	GO:0030163	protein catabolic process	125	1030	4.013e-03
GO:BP	GO:0018193	peptidyl-amino acid modification	89	686	4.115e-03
GO:BP	GO:1903522	regulation of blood circulation	41	256	4.116e-03
GO:BP	GO:0009145	purine nucleoside triphosphate biosynthetic process	23	114	4.229e-03
GO:BP	GO:2000377	regulation of reactive oxygen species metabolic process	27	144	4.247e-03
GO:BP	GO:0008154	actin polymerization or depolymerization	33	191	4.250e-03
GO:BP	GO:0051651	maintenance of location in cell	35	208	4.623e-03
GO:BP	GO:0006006	glucose metabolic process	32	184	4.670e-03
GO:BP	GO:0050804	modulation of chemical synaptic transmission	70	513	4.706e-03
GO:BP	GO:0006629	lipid metabolic process	161	1391	4.788e-03
GO:BP	GO:0010810	regulation of cell-substrate adhesion	36	217	4.935e-03
GO:BP	GO:0099177	regulation of trans-synaptic signaling	70	514	4.935e-03
GO:BP	GO:0051146	striated muscle cell differentiation	46	301	4.951e-03
GO:BP	GO:0051130	positive regulation of cellular component organization	132	1105	4.974e-03
GO:BP	GO:0050770	regulation of axonogenesis	27	146	5.192e-03
GO:BP	GO:0006816	calcium ion transport	61	434	5.300e-03
GO:BP	GO:1904064	positive regulation of cation transmembrane transport	25	131	5.300e-03
GO:BP	GO:0007229	integrin-mediated signaling pathway	23	116	5.300e-03
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	41	260	5.424e-03
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	41	260	5.424e-03
GO:BP	GO:0043270	positive regulation of monoatomic ion transport	34	202	5.424e-03
GO:BP	GO:0008064	regulation of actin polymerization or depolymerization	27	147	5.673e-03
GO:BP	GO:0019222	regulation of metabolic process	688	7035	5.673e-03
GO:BP	GO:0051648	vesicle localization	36	219	5.675e-03
GO:BP	GO:0090504	epiboly	12	42	5.713e-03
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	82	629	5.790e-03
GO:BP	GO:0051279	regulation of release of sequestered calcium ion into cytosol	18	81	5.790e-03
GO:BP	GO:0007492	endoderm development	19	88	5.790e-03
GO:BP	GO:0007417	central nervous system development	127	1061	5.790e-03
GO:BP	GO:0051640	organelle localization	81	620	5.876e-03
GO:BP	GO:1902903	regulation of supramolecular fiber organization	55	383	5.969e-03
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	343	3288	6.239e-03
GO:BP	GO:0061024	membrane organization	102	821	6.370e-03
GO:BP	GO:0098869	cellular oxidant detoxification	20	96	6.494e-03
GO:BP	GO:0033275	actin-myosin filament sliding	7	16	6.665e-03
GO:BP	GO:0009790	embryo development	134	1135	6.834e-03
GO:BP	GO:0006551	L-leucine metabolic process	5	8	6.842e-03
GO:BP	GO:0062196	regulation of lysosome size	5	8	6.842e-03
GO:BP	GO:0016052	carbohydrate catabolic process	30	173	6.990e-03
GO:BP	GO:0007626	locomotory behavior	36	222	7.048e-03
GO:BP	GO:0010001	glial cell differentiation	41	264	7.048e-03
GO:BP	GO:0009201	ribonucleoside triphosphate biosynthetic process	23	119	7.188e-03
GO:BP	GO:0008610	lipid biosynthetic process	92	729	7.274e-03
GO:BP	GO:0050801	monoatomic ion homeostasis	80	616	7.370e-03
GO:BP	GO:0072593	reactive oxygen species metabolic process	37	231	7.370e-03
GO:BP	GO:0030832	regulation of actin filament length	27	150	7.371e-03
GO:BP	GO:0043066	negative regulation of apoptotic process	107	874	7.461e-03
GO:BP	GO:0009142	nucleoside triphosphate biosynthetic process	24	127	7.461e-03
GO:BP	GO:0072522	purine-containing compound biosynthetic process	40	257	7.725e-03
GO:BP	GO:0001936	regulation of endothelial cell proliferation	25	135	7.725e-03
GO:BP	GO:0007610	behavior	86	674	7.778e-03
GO:BP	GO:0001932	regulation of protein phosphorylation	97	779	7.820e-03
GO:BP	GO:0034767	positive regulation of monoatomic ion transmembrane transport	26	143	7.882e-03
GO:BP	GO:0031103	axon regeneration	13	50	7.968e-03
GO:BP	GO:0141124	intracellular signaling cassette	210	1912	8.633e-03
GO:BP	GO:0006470	protein dephosphorylation	26	144	8.744e-03
GO:BP	GO:0016358	dendrite development	38	242	8.858e-03
GO:BP	GO:0042773	ATP synthesis coupled electron transport	20	99	9.131e-03
GO:BP	GO:0048738	cardiac muscle tissue development	37	234	9.131e-03
GO:BP	GO:0046394	carboxylic acid biosynthetic process	47	320	9.131e-03
GO:BP	GO:0042775	mitochondrial ATP synthesis coupled electron transport	20	99	9.131e-03
GO:BP	GO:0006508	proteolysis	168	1486	9.138e-03
GO:BP	GO:0045214	sarcomere organization	13	51	9.504e-03
GO:BP	GO:0071320	cellular response to cAMP	13	51	9.504e-03
GO:BP	GO:0010649	regulation of cell communication by electrical coupling	7	17	9.504e-03
GO:BP	GO:0051235	maintenance of location	35	218	9.521e-03
GO:BP	GO:2001257	regulation of cation channel activity	18	85	9.541e-03
GO:BP	GO:0072524	pyridine-containing compound metabolic process	29	169	9.541e-03
GO:BP	GO:0009152	purine ribonucleotide biosynthetic process	28	161	9.541e-03
GO:BP	GO:1990748	cellular detoxification	23	122	9.541e-03
GO:BP	GO:0030041	actin filament polymerization	28	161	9.541e-03
GO:BP	GO:0034764	positive regulation of transmembrane transport	33	202	9.861e-03
GO:BP	GO:0031346	positive regulation of cell projection organization	51	357	9.864e-03
GO:BP	GO:0010453	regulation of cell fate commitment	12	45	9.869e-03
GO:BP	GO:0051924	regulation of calcium ion transport	38	244	9.888e-03
GO:BP	GO:0022904	respiratory electron transport chain	22	115	1.011e-02
GO:BP	GO:0060627	regulation of vesicle-mediated transport	70	531	1.031e-02
GO:BP	GO:0055080	monoatomic cation homeostasis	78	606	1.036e-02
GO:BP	GO:0051129	negative regulation of cellular component organization	88	701	1.041e-02
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	46	314	1.047e-02
GO:BP	GO:0035295	tube development	129	1101	1.052e-02
GO:BP	GO:1902531	regulation of intracellular signal transduction	213	1953	1.053e-02
GO:BP	GO:0016053	organic acid biosynthetic process	47	323	1.053e-02
GO:BP	GO:0051928	positive regulation of calcium ion transport	22	116	1.119e-02
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	27	155	1.122e-02
GO:BP	GO:0046034	ATP metabolic process	36	229	1.122e-02
GO:BP	GO:0099173	postsynapse organization	38	246	1.123e-02
GO:BP	GO:0001568	blood vessel development	91	732	1.126e-02
GO:BP	GO:0009725	response to hormone	109	907	1.136e-02
GO:BP	GO:0051280	negative regulation of release of sequestered calcium ion into cytosol	6	13	1.136e-02
GO:BP	GO:0006090	pyruvate metabolic process	23	124	1.136e-02
GO:BP	GO:0032880	regulation of protein localization	109	907	1.136e-02
GO:BP	GO:0099504	synaptic vesicle cycle	35	221	1.136e-02
GO:BP	GO:0009078	pyruvate family amino acid metabolic process	6	13	1.136e-02
GO:BP	GO:0010977	negative regulation of neuron projection development	24	132	1.167e-02
GO:BP	GO:0043604	amide biosynthetic process	29	172	1.186e-02
GO:BP	GO:0014745	negative regulation of muscle adaptation	5	9	1.186e-02
GO:BP	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	5	9	1.186e-02
GO:BP	GO:0001558	regulation of cell growth	56	406	1.187e-02
GO:BP	GO:0043407	negative regulation of MAP kinase activity	11	40	1.194e-02
GO:BP	GO:0007611	learning or memory	42	282	1.217e-02
GO:BP	GO:0007369	gastrulation	32	197	1.217e-02
GO:BP	GO:0006281	DNA repair	79	621	1.265e-02
GO:BP	GO:0097553	calcium ion transmembrane import into cytosol	30	181	1.265e-02
GO:BP	GO:0048640	negative regulation of developmental growth	19	95	1.273e-02
GO:BP	GO:0042552	myelination	27	157	1.300e-02
GO:BP	GO:0060560	developmental growth involved in morphogenesis	37	240	1.301e-02
GO:BP	GO:1901698	response to nitrogen compound	126	1080	1.335e-02
GO:BP	GO:1901019	regulation of calcium ion transmembrane transporter activity	14	60	1.335e-02
GO:BP	GO:1903828	negative regulation of protein localization	34	215	1.335e-02
GO:BP	GO:0048678	response to axon injury	17	81	1.354e-02
GO:BP	GO:0014888	striated muscle adaptation	12	47	1.357e-02
GO:BP	GO:0022900	electron transport chain	23	126	1.357e-02
GO:BP	GO:0032409	regulation of transporter activity	30	182	1.357e-02
GO:BP	GO:0014909	smooth muscle cell migration	16	74	1.358e-02
GO:BP	GO:0051258	protein polymerization	42	284	1.358e-02
GO:BP	GO:1902683	regulation of receptor localization to synapse	9	29	1.384e-02
GO:BP	GO:0035767	endothelial cell chemotaxis	9	29	1.384e-02
GO:BP	GO:0014741	negative regulation of muscle hypertrophy	9	29	1.384e-02
GO:BP	GO:0000302	response to reactive oxygen species	32	199	1.384e-02
GO:BP	GO:0001935	endothelial cell proliferation	27	158	1.384e-02
GO:BP	GO:1901701	cellular response to oxygen-containing compound	136	1182	1.398e-02
GO:BP	GO:0099536	synaptic signaling	98	807	1.404e-02
GO:BP	GO:0044319	wound healing, spreading of cells	11	41	1.404e-02
GO:BP	GO:0090505	epiboly involved in wound healing	11	41	1.404e-02
GO:BP	GO:0009117	nucleotide metabolic process	65	493	1.415e-02
GO:BP	GO:0014808	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	10	35	1.427e-02
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	37	242	1.442e-02
GO:BP	GO:0030301	cholesterol transport	20	104	1.465e-02
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	45	312	1.466e-02
GO:BP	GO:0051650	establishment of vesicle localization	32	200	1.470e-02
GO:BP	GO:0051960	regulation of nervous system development	61	457	1.475e-02
GO:BP	GO:0007272	ensheathment of neurons	27	159	1.476e-02
GO:BP	GO:0008366	axon ensheathment	27	159	1.476e-02
GO:BP	GO:0043462	regulation of ATP-dependent activity	14	61	1.490e-02
GO:BP	GO:0021817	nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration	3	3	1.491e-02
GO:BP	GO:0016051	carbohydrate biosynthetic process	31	192	1.491e-02
GO:BP	GO:0006163	purine nucleotide metabolic process	58	430	1.499e-02
GO:BP	GO:0060537	muscle tissue development	58	430	1.499e-02
GO:BP	GO:0071450	cellular response to oxygen radical	8	24	1.540e-02
GO:BP	GO:0042325	regulation of phosphorylation	100	830	1.540e-02
GO:BP	GO:0071451	cellular response to superoxide	8	24	1.540e-02
GO:BP	GO:0008283	cell population proliferation	217	2015	1.540e-02
GO:BP	GO:0009636	response to toxic substance	38	252	1.540e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	105	879	1.540e-02
GO:BP	GO:0070588	calcium ion transmembrane transport	48	340	1.540e-02
GO:BP	GO:0006665	sphingolipid metabolic process	28	168	1.552e-02
GO:BP	GO:0051241	negative regulation of multicellular organismal process	126	1087	1.552e-02
GO:BP	GO:0030833	regulation of actin filament polymerization	23	128	1.556e-02
GO:BP	GO:0030049	muscle filament sliding	6	14	1.564e-02
GO:BP	GO:0030497	fatty acid elongation	6	14	1.564e-02
GO:BP	GO:0030048	actin filament-based movement	24	136	1.566e-02
GO:BP	GO:1905475	regulation of protein localization to membrane	31	193	1.566e-02
GO:BP	GO:0046959	habituation	4	6	1.624e-02
GO:BP	GO:0042981	regulation of apoptotic process	163	1462	1.626e-02
GO:BP	GO:0045785	positive regulation of cell adhesion	64	488	1.651e-02
GO:BP	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	9	30	1.660e-02
GO:BP	GO:0046621	negative regulation of organ growth	9	30	1.660e-02
GO:BP	GO:0009150	purine ribonucleotide metabolic process	49	351	1.693e-02
GO:BP	GO:0051493	regulation of cytoskeleton organization	67	517	1.719e-02
GO:BP	GO:0018209	peptidyl-serine modification	30	186	1.729e-02
GO:BP	GO:0030001	metal ion transport	105	883	1.729e-02
GO:BP	GO:0007160	cell-matrix adhesion	36	237	1.751e-02
GO:BP	GO:1903034	regulation of response to wounding	28	170	1.805e-02
GO:BP	GO:0060322	head development	97	806	1.811e-02
GO:BP	GO:0070303	negative regulation of stress-activated protein kinase signaling cascade	5	10	1.842e-02
GO:BP	GO:0009891	positive regulation of biosynthetic process	281	2696	1.843e-02
GO:BP	GO:0010927	cellular component assembly involved in morphogenesis	24	138	1.843e-02
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	52	380	1.843e-02
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	24	138	1.843e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	24	138	1.843e-02
GO:BP	GO:0019693	ribose phosphate metabolic process	52	380	1.843e-02
GO:BP	GO:0050921	positive regulation of chemotaxis	25	146	1.843e-02
GO:BP	GO:0032411	positive regulation of transporter activity	16	77	1.857e-02
GO:BP	GO:1990874	vascular associated smooth muscle cell proliferation	14	63	1.893e-02
GO:BP	GO:0006518	peptide metabolic process	14	63	1.893e-02
GO:BP	GO:0006259	DNA metabolic process	117	1005	1.893e-02
GO:BP	GO:0051281	positive regulation of release of sequestered calcium ion into cytosol	11	43	1.898e-02
GO:BP	GO:0072659	protein localization to plasma membrane	42	291	1.898e-02
GO:BP	GO:2001259	positive regulation of cation channel activity	11	43	1.898e-02
GO:BP	GO:0022898	regulation of transmembrane transporter activity	28	171	1.904e-02
GO:BP	GO:0061572	actin filament bundle organization	27	163	1.931e-02
GO:BP	GO:0034504	protein localization to nucleus	45	318	1.931e-02
GO:BP	GO:0032412	regulation of monoatomic ion transmembrane transporter activity	27	163	1.931e-02
GO:BP	GO:1903514	release of sequestered calcium ion into cytosol by endoplasmic reticulum	10	37	1.998e-02
GO:BP	GO:0008654	phospholipid biosynthetic process	38	257	2.027e-02
GO:BP	GO:1901136	carbohydrate derivative catabolic process	38	257	2.027e-02
GO:BP	GO:0099537	trans-synaptic signaling	94	781	2.042e-02
GO:BP	GO:0014037	Schwann cell differentiation	12	50	2.045e-02
GO:BP	GO:0032386	regulation of intracellular transport	39	266	2.050e-02
GO:BP	GO:0001764	neuron migration	30	189	2.100e-02
GO:BP	GO:1990778	protein localization to cell periphery	50	365	2.119e-02
GO:BP	GO:1901700	response to oxygen-containing compound	182	1669	2.119e-02
GO:BP	GO:0048008	platelet-derived growth factor receptor signaling pathway	13	57	2.119e-02
GO:BP	GO:0045780	positive regulation of bone resorption	7	20	2.123e-02
GO:BP	GO:0014074	response to purine-containing compound	25	148	2.135e-02
GO:BP	GO:0007267	cell-cell signaling	150	1342	2.141e-02
GO:BP	GO:0097237	cellular response to toxic substance	23	132	2.144e-02
GO:BP	GO:0051956	negative regulation of amino acid transport	6	15	2.144e-02
GO:BP	GO:0051284	positive regulation of sequestering of calcium ion	6	15	2.144e-02
GO:BP	GO:2001028	positive regulation of endothelial cell chemotaxis	6	15	2.144e-02
GO:BP	GO:0015850	organic hydroxy compound transport	39	267	2.144e-02
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	68	533	2.166e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	86	706	2.204e-02
GO:BP	GO:0042398	modified amino acid biosynthetic process	11	44	2.204e-02
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	67	524	2.204e-02
GO:BP	GO:0071840	cellular component organization or biogenesis	799	8393	2.239e-02
GO:BP	GO:0015918	sterol transport	20	109	2.240e-02
GO:BP	GO:0098771	inorganic ion homeostasis	68	534	2.245e-02
GO:BP	GO:0007268	chemical synaptic transmission	93	775	2.259e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	93	775	2.259e-02
GO:BP	GO:0032271	regulation of protein polymerization	31	199	2.289e-02
GO:BP	GO:0018105	peptidyl-serine phosphorylation	28	174	2.330e-02
GO:BP	GO:0032781	positive regulation of ATP-dependent activity	10	38	2.346e-02
GO:BP	GO:0071901	negative regulation of protein serine/threonine kinase activity	15	72	2.352e-02
GO:BP	GO:0009628	response to abiotic stimulus	130	1144	2.357e-02
GO:BP	GO:0007163	establishment or maintenance of cell polarity	35	234	2.387e-02
GO:BP	GO:0006754	ATP biosynthetic process	19	102	2.387e-02
GO:BP	GO:0071295	cellular response to vitamin	9	32	2.415e-02
GO:BP	GO:0046390	ribose phosphate biosynthetic process	29	183	2.421e-02
GO:BP	GO:0008361	regulation of cell size	29	183	2.421e-02
GO:BP	GO:0021782	glial cell development	23	134	2.508e-02
GO:BP	GO:0032868	response to insulin	39	270	2.530e-02
GO:BP	GO:0055013	cardiac muscle cell development	16	80	2.545e-02
GO:BP	GO:0033273	response to vitamin	18	95	2.545e-02
GO:BP	GO:0010038	response to metal ion	48	351	2.545e-02
GO:BP	GO:0034446	substrate adhesion-dependent cell spreading	19	103	2.641e-02
GO:BP	GO:0050790	regulation of catalytic activity	108	928	2.646e-02
GO:BP	GO:0009260	ribonucleotide biosynthetic process	28	176	2.688e-02
GO:BP	GO:0051036	regulation of endosome size	5	11	2.702e-02
GO:BP	GO:0044062	regulation of excretion	5	11	2.702e-02
GO:BP	GO:0072015	podocyte development	5	11	2.702e-02
GO:BP	GO:0014812	muscle cell migration	17	88	2.702e-02
GO:BP	GO:0010881	regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion	7	21	2.710e-02
GO:BP	GO:0051094	positive regulation of developmental process	149	1343	2.765e-02
GO:BP	GO:0071711	basement membrane organization	10	39	2.779e-02
GO:BP	GO:0045926	negative regulation of growth	34	228	2.797e-02
GO:BP	GO:0007612	learning	26	160	2.797e-02
GO:BP	GO:0051017	actin filament bundle assembly	26	160	2.797e-02
GO:BP	GO:0009259	ribonucleotide metabolic process	50	372	2.897e-02
GO:BP	GO:0048842	positive regulation of axon extension involved in axon guidance	4	7	2.905e-02
GO:BP	GO:0098877	neurotransmitter receptor transport to plasma membrane	6	16	2.909e-02
GO:BP	GO:0010801	negative regulation of peptidyl-threonine phosphorylation	6	16	2.909e-02
GO:BP	GO:0030167	proteoglycan catabolic process	6	16	2.909e-02
GO:BP	GO:0000303	response to superoxide	8	27	2.913e-02
GO:BP	GO:0010614	negative regulation of cardiac muscle hypertrophy	8	27	2.913e-02
GO:BP	GO:0010594	regulation of endothelial cell migration	27	169	2.924e-02
GO:BP	GO:0006898	receptor-mediated endocytosis	38	264	2.927e-02
GO:BP	GO:0032964	collagen biosynthetic process	11	46	2.971e-02
GO:BP	GO:0007599	hemostasis	35	238	3.004e-02
GO:BP	GO:0014910	regulation of smooth muscle cell migration	14	67	3.029e-02
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	14	67	3.029e-02
GO:BP	GO:0051403	stress-activated MAPK cascade	12	53	3.070e-02
GO:BP	GO:0043113	receptor clustering	13	60	3.073e-02
GO:BP	GO:0043542	endothelial cell migration	33	221	3.073e-02
GO:BP	GO:0050890	cognition	45	328	3.104e-02
GO:BP	GO:0033673	negative regulation of kinase activity	24	145	3.104e-02
GO:BP	GO:0010498	proteasomal protein catabolic process	68	543	3.115e-02
GO:BP	GO:0007613	memory	22	129	3.179e-02
GO:BP	GO:0019362	pyridine nucleotide metabolic process	26	162	3.208e-02
GO:BP	GO:0046496	nicotinamide nucleotide metabolic process	26	162	3.208e-02
GO:BP	GO:0043254	regulation of protein-containing complex assembly	55	421	3.215e-02
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	268	2593	3.216e-02
GO:BP	GO:0070925	organelle assembly	119	1046	3.231e-02
GO:BP	GO:0014911	positive regulation of smooth muscle cell migration	10	40	3.231e-02
GO:BP	GO:0046777	protein autophosphorylation	28	179	3.231e-02
GO:BP	GO:0043434	response to peptide hormone	57	440	3.233e-02
GO:BP	GO:0072384	organelle transport along microtubule	17	90	3.238e-02
GO:BP	GO:0098609	cell-cell adhesion	112	976	3.238e-02
GO:BP	GO:0010647	positive regulation of cell communication	192	1795	3.272e-02
GO:BP	GO:0007584	response to nutrient	27	171	3.314e-02
GO:BP	GO:1990138	neuron projection extension	27	171	3.314e-02
GO:BP	GO:0023056	positive regulation of signaling	192	1796	3.337e-02
GO:BP	GO:0098801	regulation of renal system process	7	22	3.375e-02
GO:BP	GO:0021762	substantia nigra development	11	47	3.375e-02
GO:BP	GO:0019430	removal of superoxide radicals	7	22	3.375e-02
GO:BP	GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	7	22	3.375e-02
GO:BP	GO:0050878	regulation of body fluid levels	50	376	3.375e-02
GO:BP	GO:0050919	negative chemotaxis	11	47	3.375e-02
GO:BP	GO:0033627	cell adhesion mediated by integrin	16	83	3.412e-02
GO:BP	GO:0046173	polyol biosynthetic process	13	61	3.416e-02
GO:BP	GO:1904705	regulation of vascular associated smooth muscle cell proliferation	13	61	3.416e-02
GO:BP	GO:0050771	negative regulation of axonogenesis	12	54	3.428e-02
GO:BP	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	12	54	3.428e-02
GO:BP	GO:0009081	branched-chain amino acid metabolic process	8	28	3.489e-02
GO:BP	GO:0000305	response to oxygen radical	8	28	3.489e-02
GO:BP	GO:0034614	cellular response to reactive oxygen species	24	147	3.532e-02
GO:BP	GO:0046364	monosaccharide biosynthetic process	17	91	3.532e-02
GO:BP	GO:0006635	fatty acid beta-oxidation	15	76	3.582e-02
GO:BP	GO:0034762	regulation of transmembrane transport	57	443	3.608e-02
GO:BP	GO:0072001	renal system development	45	332	3.676e-02
GO:BP	GO:0010595	positive regulation of endothelial cell migration	19	107	3.676e-02
GO:BP	GO:0050767	regulation of neurogenesis	50	378	3.676e-02
GO:BP	GO:0043405	regulation of MAP kinase activity	20	115	3.687e-02
GO:BP	GO:0042254	ribosome biogenesis	44	323	3.692e-02
GO:BP	GO:0014733	regulation of skeletal muscle adaptation	5	12	3.738e-02
GO:BP	GO:1901844	regulation of cell communication by electrical coupling involved in cardiac conduction	5	12	3.738e-02
GO:BP	GO:0051386	regulation of neurotrophin TRK receptor signaling pathway	5	12	3.738e-02
GO:BP	GO:1903909	regulation of receptor clustering	6	17	3.738e-02
GO:BP	GO:2000009	negative regulation of protein localization to cell surface	5	12	3.738e-02
GO:BP	GO:0099515	actin filament-based transport	5	12	3.738e-02
GO:BP	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	5	12	3.738e-02
GO:BP	GO:0006094	gluconeogenesis	16	84	3.738e-02
GO:BP	GO:0018126	protein hydroxylation	6	17	3.738e-02
GO:BP	GO:0043589	skin morphogenesis	5	12	3.738e-02
GO:BP	GO:0072310	glomerular epithelial cell development	5	12	3.738e-02
GO:BP	GO:0060414	aorta smooth muscle tissue morphogenesis	3	4	3.817e-02
GO:BP	GO:0042822	pyridoxal phosphate metabolic process	3	4	3.817e-02
GO:BP	GO:0060024	rhythmic synaptic transmission	3	4	3.817e-02
GO:BP	GO:0001938	positive regulation of endothelial cell proliferation	17	92	3.817e-02
GO:BP	GO:0006273	lagging strand elongation	3	4	3.817e-02
GO:BP	GO:1905749	regulation of endosome to plasma membrane protein transport	3	4	3.817e-02
GO:BP	GO:0030207	chondroitin sulfate proteoglycan catabolic process	3	4	3.817e-02
GO:BP	GO:0007420	brain development	89	754	3.817e-02
GO:BP	GO:0046166	glyceraldehyde-3-phosphate biosynthetic process	3	4	3.817e-02
GO:BP	GO:0050805	negative regulation of synaptic transmission	12	55	3.817e-02
GO:BP	GO:0061041	regulation of wound healing	22	132	3.834e-02
GO:BP	GO:0032368	regulation of lipid transport	22	132	3.834e-02
GO:BP	GO:0046683	response to organophosphorus	22	132	3.834e-02
GO:BP	GO:0050773	regulation of dendrite development	18	100	3.856e-02
GO:BP	GO:0048584	positive regulation of response to stimulus	242	2331	3.868e-02
GO:BP	GO:0031952	regulation of protein autophosphorylation	9	35	3.926e-02
GO:BP	GO:0098754	detoxification	24	149	3.983e-02
GO:BP	GO:0051093	negative regulation of developmental process	106	925	3.988e-02
GO:BP	GO:0032414	positive regulation of ion transmembrane transporter activity	14	70	4.073e-02
GO:BP	GO:0006801	superoxide metabolic process	14	70	4.073e-02
GO:BP	GO:1904706	negative regulation of vascular associated smooth muscle cell proliferation	7	23	4.085e-02
GO:BP	GO:0033043	regulation of organelle organization	128	1148	4.085e-02
GO:BP	GO:0032891	negative regulation of organic acid transport	7	23	4.085e-02
GO:BP	GO:1901020	negative regulation of calcium ion transmembrane transporter activity	7	23	4.085e-02
GO:BP	GO:0070296	sarcoplasmic reticulum calcium ion transport	10	42	4.227e-02
GO:BP	GO:0061387	regulation of extent of cell growth	18	101	4.227e-02
GO:BP	GO:0048144	fibroblast proliferation	19	109	4.251e-02
GO:BP	GO:0007623	circadian rhythm	31	210	4.285e-02
GO:BP	GO:0006935	chemotaxis	59	467	4.285e-02
GO:BP	GO:0015986	proton motive force-driven ATP synthesis	15	78	4.294e-02
GO:BP	GO:1903169	regulation of calcium ion transmembrane transport	26	167	4.299e-02
GO:BP	GO:0043536	positive regulation of blood vessel endothelial cell migration	12	56	4.299e-02
GO:BP	GO:0086065	cell communication involved in cardiac conduction	12	56	4.299e-02
GO:BP	GO:0048662	negative regulation of smooth muscle cell proliferation	11	49	4.306e-02
GO:BP	GO:0006164	purine nucleotide biosynthetic process	29	193	4.371e-02
GO:BP	GO:0055006	cardiac cell development	16	86	4.422e-02
GO:BP	GO:0006633	fatty acid biosynthetic process	25	159	4.422e-02
GO:BP	GO:0044042	glucan metabolic process	16	86	4.422e-02
GO:BP	GO:0032456	endocytic recycling	16	86	4.422e-02
GO:BP	GO:0050769	positive regulation of neurogenesis	35	246	4.422e-02
GO:BP	GO:0035813	regulation of renal sodium excretion	4	8	4.423e-02
GO:BP	GO:0045859	regulation of protein kinase activity	52	402	4.423e-02
GO:BP	GO:0017185	peptidyl-lysine hydroxylation	4	8	4.423e-02
GO:BP	GO:0014722	regulation of skeletal muscle contraction by calcium ion signaling	4	8	4.423e-02
GO:BP	GO:0014052	regulation of gamma-aminobutyric acid secretion	4	8	4.423e-02
GO:BP	GO:0042330	taxis	59	469	4.546e-02
GO:BP	GO:0048638	regulation of developmental growth	42	310	4.546e-02
GO:BP	GO:0005976	polysaccharide metabolic process	18	102	4.546e-02
GO:BP	GO:0019058	viral life cycle	42	310	4.546e-02
GO:BP	GO:0072526	pyridine-containing compound catabolic process	18	102	4.546e-02
GO:BP	GO:0006099	tricarboxylic acid cycle	9	36	4.557e-02
GO:BP	GO:0050817	coagulation	34	238	4.600e-02
GO:BP	GO:0009887	animal organ morphogenesis	117	1042	4.607e-02
GO:BP	GO:0048659	smooth muscle cell proliferation	23	143	4.621e-02
GO:BP	GO:0051253	negative regulation of RNA metabolic process	152	1400	4.622e-02
GO:BP	GO:0097120	receptor localization to synapse	15	79	4.640e-02
GO:BP	GO:0099518	vesicle cytoskeletal trafficking	13	64	4.640e-02
GO:BP	GO:0045722	positive regulation of gluconeogenesis	6	18	4.640e-02
GO:BP	GO:0002011	morphogenesis of an epithelial sheet	13	64	4.640e-02
GO:BP	GO:1902170	cellular response to reactive nitrogen species	6	18	4.640e-02
GO:BP	GO:0050772	positive regulation of axonogenesis	15	79	4.640e-02
GO:BP	GO:0031098	stress-activated protein kinase signaling cascade	12	57	4.739e-02
GO:BP	GO:0035088	establishment or maintenance of apical/basal cell polarity	12	57	4.739e-02
GO:BP	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	10	43	4.739e-02
GO:BP	GO:0099084	postsynaptic specialization organization	12	57	4.739e-02
GO:BP	GO:0046839	phospholipid dephosphorylation	10	43	4.739e-02
GO:BP	GO:0061245	establishment or maintenance of bipolar cell polarity	12	57	4.739e-02
GO:BP	GO:0048010	vascular endothelial growth factor receptor signaling pathway	12	57	4.739e-02
GO:BP	GO:0043086	negative regulation of catalytic activity	40	293	4.742e-02
GO:BP	GO:0140238	presynaptic endocytosis	16	87	4.742e-02
GO:BP	GO:0019319	hexose biosynthetic process	16	87	4.742e-02
GO:BP	GO:0048514	blood vessel morphogenesis	76	635	4.744e-02
GO:BP	GO:1904062	regulation of monoatomic cation transmembrane transport	39	284	4.752e-02
GO:BP	GO:0048668	collateral sprouting	8	30	4.779e-02
GO:BP	GO:0006096	glycolytic process	17	95	4.815e-02
GO:BP	GO:0070252	actin-mediated cell contraction	19	111	4.838e-02
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	18	103	4.841e-02
GO:BP	GO:0042659	regulation of cell fate specification	7	24	4.854e-02
GO:BP	GO:0043501	skeletal muscle adaptation	7	24	4.854e-02
GO:BP	GO:0036119	response to platelet-derived growth factor	7	24	4.854e-02
GO:BP	GO:0044409	symbiont entry into host	23	144	4.854e-02
GO:BP	GO:0032272	negative regulation of protein polymerization	14	72	4.854e-02
GO:BP	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	5	13	4.902e-02
GO:BP	GO:0010745	negative regulation of macrophage derived foam cell differentiation	5	13	4.902e-02
GO:BP	GO:0007596	blood coagulation	33	231	4.965e-02
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	164	1529	5.000e-02
KEGG	KEGG:04260	Cardiac muscle contraction	29	87	6.023e-06
KEGG	KEGG:01100	Metabolic pathways	227	1537	2.121e-05
KEGG	KEGG:04512	ECM-receptor interaction	28	89	2.121e-05
KEGG	KEGG:05208	Chemical carcinogenesis - reactive oxygen species	50	221	2.905e-05
KEGG	KEGG:05415	Diabetic cardiomyopathy	46	202	4.712e-05
KEGG	KEGG:04510	Focal adhesion	46	202	4.712e-05
KEGG	KEGG:01200	Carbon metabolism	31	115	6.136e-05
KEGG	KEGG:05016	Huntington disease	61	305	6.731e-05
KEGG	KEGG:00190	Oxidative phosphorylation	34	134	6.731e-05
KEGG	KEGG:05012	Parkinson disease	54	265	1.277e-04
KEGG	KEGG:05414	Dilated cardiomyopathy	27	102	2.721e-04
KEGG	KEGG:05410	Hypertrophic cardiomyopathy	26	97	2.854e-04
KEGG	KEGG:04714	Thermogenesis	47	232	4.905e-04
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	80	474	9.798e-04
KEGG	KEGG:05020	Prion disease	51	271	1.510e-03
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	32	153	4.572e-03
KEGG	KEGG:01230	Biosynthesis of amino acids	19	74	5.697e-03
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	61	363	7.134e-03
KEGG	KEGG:04922	Glucagon signaling pathway	24	107	7.951e-03
KEGG	KEGG:01210	2-Oxocarboxylic acid metabolism	11	33	8.279e-03
KEGG	KEGG:05010	Alzheimer disease	63	382	8.279e-03
KEGG	KEGG:04932	Non-alcoholic fatty liver disease	31	154	8.362e-03
KEGG	KEGG:04910	Insulin signaling pathway	28	137	1.137e-02
KEGG	KEGG:00630	Glyoxylate and dicarboxylate metabolism	10	30	1.299e-02
KEGG	KEGG:05412	Arrhythmogenic right ventricular cardiomyopathy	19	84	1.921e-02
KEGG	KEGG:00280	Valine, leucine and isoleucine degradation	13	48	1.921e-02
KEGG	KEGG:05165	Human papillomavirus infection	54	330	1.921e-02
KEGG	KEGG:04925	Aldosterone synthesis and secretion	21	98	2.218e-02
KEGG	KEGG:04722	Neurotrophin signaling pathway	24	118	2.234e-02
KEGG	KEGG:00480	Glutathione metabolism	14	56	2.609e-02
KEGG	KEGG:04810	Regulation of actin cytoskeleton	39	227	2.934e-02
KEGG	KEGG:01212	Fatty acid metabolism	14	57	2.934e-02
KEGG	KEGG:03050	Proteasome	12	46	3.271e-02
KEGG	KEGG:00020	Citrate cycle (TCA cycle)	9	30	3.725e-02
KEGG	KEGG:05222	Small cell lung cancer	19	92	4.297e-02
KEGG	KEGG:05200	Pathways in cancer	77	527	4.297e-02

#GO:BP
table_DOX24R_genes_GOBP <- table_DOX24R_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24R_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24R Specific DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24R_genes_KEGG <- table_DOX24R_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24R_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24R DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX144R DEGs GO KEGG#####
# D144R_DEGs_mat <- as.matrix(DOX144R_DEGs_GO)
# 
# DOX_144R_dxr_gene <- gost(query = D144R_DEGs_mat,
#                       organism = "hsapiens",
#                       ordered_query = FALSE,
#                       measure_underrepresentation = FALSE,
#                       evcodes = FALSE,
#                       user_threshold = 0.05,
#                       correction_method = c("fdr"),
#                       sources = c("GO:BP", "KEGG"))
# 
# DOX_144R_gost_genes <- gostplot(DOX_144R_dxr_gene, capped = FALSE, interactive = TRUE)
# DOX_144R_gost_genes
# 
# table_DOX144R_genes <- DOX_144R_dxr_gene$result %>% 
#   dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))
# 
# table_DOX144R_genes %>% 
#   mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
#   kableExtra::kable(.,) %>% 
#   kableExtra::kable_paper("striped", full_width = FALSE) %>% 
#   kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
#   kableExtra::scroll_box(width = "100%", height = "400px")
# 
# #GO:BP
# table_DOX144R_genes_GOBP <- table_DOX144R_genes %>% 
#   dplyr::filter(source=="GO:BP") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX144R_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX144R Specific DEGs Enriched GO:BP Terms")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("GO:BP term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))
# 
# #KEGG
# table_DOX144R_genes_KEGG <- table_DOX144R_genes %>% 
#   dplyr::filter(source=="KEGG") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX144R_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX144R DEGs Enriched KEGG Terms")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("KEGG term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))

#####DOX144R shared DEGs GO KEGG#####
D144Rshare_DEGs_mat <- as.matrix(DOX144Rshare_DEGs_GO_plot)

DOX_144Rshare_dxr_gene <- gost(query = D144Rshare_DEGs_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_144Rshare_gost_genes <- gostplot(DOX_144Rshare_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_144Rshare_gost_genes

table_DOX144Rshare_genes <- DOX_144Rshare_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX144Rshare_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0022402	cell cycle process	169	1280	8.265e-83
GO:BP	GO:0007049	cell cycle	180	1663	5.991e-75
GO:BP	GO:1903047	mitotic cell cycle process	128	745	1.284e-74
GO:BP	GO:0000278	mitotic cell cycle	135	892	5.412e-72
GO:BP	GO:0007059	chromosome segregation	97	427	4.095e-67
GO:BP	GO:0051301	cell division	104	658	7.689e-56
GO:BP	GO:0000280	nuclear division	89	452	1.399e-55
GO:BP	GO:0098813	nuclear chromosome segregation	78	323	1.859e-55
GO:BP	GO:0010564	regulation of cell cycle process	107	720	5.055e-55
GO:BP	GO:0048285	organelle fission	90	500	7.171e-53
GO:BP	GO:0051276	chromosome organization	94	574	1.210e-51
GO:BP	GO:0140014	mitotic nuclear division	70	282	1.752e-50
GO:BP	GO:0000070	mitotic sister chromatid segregation	60	193	2.327e-49
GO:BP	GO:0000819	sister chromatid segregation	64	234	6.805e-49
GO:BP	GO:0051726	regulation of cell cycle	120	1087	3.086e-48
GO:BP	GO:0044770	cell cycle phase transition	85	532	1.429e-45
GO:BP	GO:1901987	regulation of cell cycle phase transition	73	427	8.453e-41
GO:BP	GO:0044772	mitotic cell cycle phase transition	72	428	9.899e-40
GO:BP	GO:0006260	DNA replication	60	283	9.020e-39
GO:BP	GO:0000075	cell cycle checkpoint signaling	49	185	2.536e-36
GO:BP	GO:0007346	regulation of mitotic cell cycle	72	492	1.354e-35
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	53	248	2.918e-34
GO:BP	GO:0051983	regulation of chromosome segregation	41	132	2.543e-33
GO:BP	GO:0006261	DNA-templated DNA replication	44	160	2.638e-33
GO:BP	GO:0006259	DNA metabolic process	97	1005	2.876e-33
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	58	327	5.204e-33
GO:BP	GO:0010948	negative regulation of cell cycle process	55	289	6.743e-33
GO:BP	GO:1905818	regulation of chromosome separation	33	77	4.239e-32
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	40	136	1.630e-31
GO:BP	GO:0051310	metaphase chromosome alignment	36	104	3.831e-31
GO:BP	GO:0051304	chromosome separation	33	84	1.299e-30
GO:BP	GO:0090068	positive regulation of cell cycle process	50	262	6.907e-30
GO:BP	GO:0007088	regulation of mitotic nuclear division	37	121	8.257e-30
GO:BP	GO:0045786	negative regulation of cell cycle	58	377	1.216e-29
GO:BP	GO:0050000	chromosome localization	37	126	4.140e-29
GO:BP	GO:0051303	establishment of chromosome localization	36	118	5.703e-29
GO:BP	GO:0006974	DNA damage response	86	908	1.113e-28
GO:BP	GO:0006281	DNA repair	71	621	2.588e-28
GO:BP	GO:0051783	regulation of nuclear division	38	149	1.940e-27
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	44	225	1.071e-26
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	27	62	1.854e-26
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	39	169	1.976e-26
GO:BP	GO:0051306	mitotic sister chromatid separation	27	65	8.610e-26
GO:BP	GO:0045787	positive regulation of cell cycle	52	351	1.042e-25
GO:BP	GO:0033045	regulation of sister chromatid segregation	32	107	2.015e-25
GO:BP	GO:0006996	organelle organization	177	3594	2.448e-25
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	25	54	2.477e-25
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	24	49	4.488e-25
GO:BP	GO:0071173	spindle assembly checkpoint signaling	24	49	4.488e-25
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	24	49	4.488e-25
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	38	172	4.616e-25
GO:BP	GO:0031577	spindle checkpoint signaling	24	50	8.130e-25
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	25	57	1.219e-24
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	24	51	1.373e-24
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	24	51	1.373e-24
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	24	51	1.373e-24
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	24	51	1.373e-24
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	30	97	2.236e-24
GO:BP	GO:0051985	negative regulation of chromosome segregation	24	53	4.178e-24
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	24	53	4.178e-24
GO:BP	GO:1905819	negative regulation of chromosome separation	24	53	4.178e-24
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	30	100	5.811e-24
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	29	93	1.084e-23
GO:BP	GO:0051321	meiotic cell cycle	46	297	1.336e-23
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	29	96	2.947e-23
GO:BP	GO:0007051	spindle organization	39	206	3.356e-23
GO:BP	GO:0033554	cellular response to stress	114	1830	7.833e-23
GO:BP	GO:1903046	meiotic cell cycle process	40	224	8.005e-23
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	24	59	9.066e-23
GO:BP	GO:0033044	regulation of chromosome organization	41	242	1.645e-22
GO:BP	GO:0007052	mitotic spindle organization	32	134	3.088e-22
GO:BP	GO:0051784	negative regulation of nuclear division	24	65	1.411e-21
GO:BP	GO:0140013	meiotic nuclear division	37	202	1.746e-21
GO:BP	GO:0044839	cell cycle G2/M phase transition	33	156	3.616e-21
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	31	139	1.389e-20
GO:BP	GO:0000226	microtubule cytoskeleton organization	62	670	7.255e-20
GO:BP	GO:2001251	negative regulation of chromosome organization	25	97	3.767e-18
GO:BP	GO:0006302	double-strand break repair	41	319	6.401e-18
GO:BP	GO:0006270	DNA replication initiation	17	37	3.948e-17
GO:BP	GO:0045132	meiotic chromosome segregation	24	96	4.416e-17
GO:BP	GO:0140694	membraneless organelle assembly	46	430	5.855e-17
GO:BP	GO:0051656	establishment of organelle localization	49	491	7.415e-17
GO:BP	GO:0031570	DNA integrity checkpoint signaling	26	123	1.366e-16
GO:BP	GO:0051225	spindle assembly	27	136	1.654e-16
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	20	63	1.906e-16
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	24	105	3.934e-16
GO:BP	GO:0061982	meiosis I cell cycle process	27	141	4.217e-16
GO:BP	GO:0034508	centromere complex assembly	15	29	4.217e-16
GO:BP	GO:0007017	microtubule-based process	70	999	6.111e-16
GO:BP	GO:0006310	DNA recombination	40	347	7.888e-16
GO:BP	GO:0051383	kinetochore organization	13	21	2.587e-15
GO:BP	GO:1905820	positive regulation of chromosome separation	15	32	2.768e-15
GO:BP	GO:0033043	regulation of organelle organization	74	1148	5.858e-15
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	24	118	6.366e-15
GO:BP	GO:0051640	organelle localization	52	620	9.313e-15
GO:BP	GO:0051128	regulation of cellular component organization	117	2433	1.266e-14
GO:BP	GO:0000725	recombinational repair	29	193	2.078e-14
GO:BP	GO:0051984	positive regulation of chromosome segregation	14	30	3.157e-14
GO:BP	GO:0051716	cellular response to stimulus	248	7376	4.246e-14
GO:BP	GO:0000724	double-strand break repair via homologous recombination	28	188	8.284e-14
GO:BP	GO:0000727	double-strand break repair via break-induced replication	10	12	8.310e-14
GO:BP	GO:0007127	meiosis I	24	133	1.031e-13
GO:BP	GO:0034502	protein localization to chromosome	23	126	3.040e-13
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	12	23	6.528e-13
GO:BP	GO:0035556	intracellular signal transduction	128	2965	1.261e-12
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	12	25	2.366e-12
GO:BP	GO:0000077	DNA damage checkpoint signaling	21	114	3.693e-12
GO:BP	GO:0033260	nuclear DNA replication	14	41	5.550e-12
GO:BP	GO:0065004	protein-DNA complex assembly	29	241	6.872e-12
GO:BP	GO:0000910	cytokinesis	26	192	7.745e-12
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	19	93	7.745e-12
GO:BP	GO:0007010	cytoskeleton organization	81	1529	8.450e-12
GO:BP	GO:0000281	mitotic cytokinesis	19	95	1.139e-11
GO:BP	GO:0006950	response to stress	153	3948	1.169e-11
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	17	74	1.835e-11
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	21	124	1.919e-11
GO:BP	GO:0044786	cell cycle DNA replication	14	45	2.236e-11
GO:BP	GO:0090307	mitotic spindle assembly	17	76	2.860e-11
GO:BP	GO:0051052	regulation of DNA metabolic process	41	500	2.907e-11
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	20	114	3.381e-11
GO:BP	GO:0016043	cellular component organization	257	8184	4.377e-11
GO:BP	GO:0071824	protein-DNA complex organization	29	262	5.211e-11
GO:BP	GO:1901976	regulation of cell cycle checkpoint	14	48	5.785e-11
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	13	40	7.637e-11
GO:BP	GO:0006275	regulation of DNA replication	20	120	8.795e-11
GO:BP	GO:0032465	regulation of cytokinesis	18	94	9.552e-11
GO:BP	GO:0050896	response to stimulus	274	8999	1.230e-10
GO:BP	GO:0010639	negative regulation of organelle organization	33	352	1.430e-10
GO:BP	GO:0019953	sexual reproduction	64	1122	1.571e-10
GO:BP	GO:0044771	meiotic cell cycle phase transition	9	15	2.056e-10
GO:BP	GO:0030174	regulation of DNA-templated DNA replication initiation	9	15	2.056e-10
GO:BP	GO:0070925	organelle assembly	60	1046	6.221e-10
GO:BP	GO:0022414	reproductive process	79	1608	6.721e-10
GO:BP	GO:0071840	cellular component organization or biogenesis	257	8393	9.106e-10
GO:BP	GO:0051382	kinetochore assembly	9	17	9.243e-10
GO:BP	GO:1902969	mitotic DNA replication	9	17	9.243e-10
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	15	70	1.092e-09
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	19	124	1.309e-09
GO:BP	GO:0051302	regulation of cell division	23	188	1.309e-09
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	12	41	1.969e-09
GO:BP	GO:0090231	regulation of spindle checkpoint	10	25	2.273e-09
GO:BP	GO:0009314	response to radiation	35	437	2.411e-09
GO:BP	GO:0007143	female meiotic nuclear division	12	42	2.645e-09
GO:BP	GO:0051231	spindle elongation	8	14	5.133e-09
GO:BP	GO:0030261	chromosome condensation	12	45	6.387e-09
GO:BP	GO:0051653	spindle localization	14	68	8.293e-09
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	9	21	9.552e-09
GO:BP	GO:0034080	CENP-A containing chromatin assembly	7	10	9.594e-09
GO:BP	GO:0031055	chromatin remodeling at centromere	7	10	9.594e-09
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	14	69	9.923e-09
GO:BP	GO:0042770	signal transduction in response to DNA damage	21	173	9.990e-09
GO:BP	GO:0006271	DNA strand elongation involved in DNA replication	8	15	1.009e-08
GO:BP	GO:0034501	protein localization to kinetochore	8	15	1.009e-08
GO:BP	GO:1903083	protein localization to condensed chromosome	8	15	1.009e-08
GO:BP	GO:0010212	response to ionizing radiation	19	141	1.135e-08
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	14	71	1.426e-08
GO:BP	GO:0050794	regulation of cellular process	330	11946	1.480e-08
GO:BP	GO:0032467	positive regulation of cytokinesis	12	50	2.237e-08
GO:BP	GO:0051256	mitotic spindle midzone assembly	7	11	2.425e-08
GO:BP	GO:0050789	regulation of biological process	337	12336	2.848e-08
GO:BP	GO:0051293	establishment of spindle localization	13	63	3.211e-08
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	9	24	3.611e-08
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	9	24	3.611e-08
GO:BP	GO:0000022	mitotic spindle elongation	7	12	5.535e-08
GO:BP	GO:1905821	positive regulation of chromosome condensation	6	8	9.384e-08
GO:BP	GO:0007076	mitotic chromosome condensation	8	19	1.016e-07
GO:BP	GO:0007062	sister chromatid cohesion	12	57	1.071e-07
GO:BP	GO:0065007	biological regulation	343	12743	1.148e-07
GO:BP	GO:0008283	cell population proliferation	85	2015	1.572e-07
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	12	59	1.599e-07
GO:BP	GO:0000076	DNA replication checkpoint signaling	8	20	1.612e-07
GO:BP	GO:0010638	positive regulation of organelle organization	34	492	1.719e-07
GO:BP	GO:0051255	spindle midzone assembly	7	14	2.187e-07
GO:BP	GO:0051130	positive regulation of cellular component organization	56	1105	2.211e-07
GO:BP	GO:1900264	positive regulation of DNA-directed DNA polymerase activity	6	9	2.604e-07
GO:BP	GO:0044843	cell cycle G1/S phase transition	22	230	3.001e-07
GO:BP	GO:0007098	centrosome cycle	17	140	4.203e-07
GO:BP	GO:0051129	negative regulation of cellular component organization	41	701	5.461e-07
GO:BP	GO:0045143	homologous chromosome segregation	12	67	6.923e-07
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	20	202	7.680e-07
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	11	55	7.878e-07
GO:BP	GO:0035825	homologous recombination	12	68	8.104e-07
GO:BP	GO:0048522	positive regulation of cellular process	185	5920	1.444e-06
GO:BP	GO:0031023	microtubule organizing center organization	17	153	1.534e-06
GO:BP	GO:0071897	DNA biosynthetic process	18	172	1.581e-06
GO:BP	GO:0051294	establishment of spindle orientation	10	47	1.760e-06
GO:BP	GO:2001252	positive regulation of chromosome organization	14	105	2.275e-06
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	9	37	2.303e-06
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	6	12	2.493e-06
GO:BP	GO:0060623	regulation of chromosome condensation	6	12	2.493e-06
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	5	7	2.763e-06
GO:BP	GO:0071478	cellular response to radiation	18	182	3.619e-06
GO:BP	GO:0009628	response to abiotic stimulus	54	1144	3.916e-06
GO:BP	GO:0090232	positive regulation of spindle checkpoint	6	13	4.426e-06
GO:BP	GO:1903490	positive regulation of mitotic cytokinesis	6	13	4.426e-06
GO:BP	GO:0070192	chromosome organization involved in meiotic cell cycle	11	66	5.239e-06
GO:BP	GO:0051781	positive regulation of cell division	13	98	6.639e-06
GO:BP	GO:0048518	positive regulation of biological process	190	6264	7.661e-06
GO:BP	GO:0000212	meiotic spindle organization	7	22	8.096e-06
GO:BP	GO:0040001	establishment of mitotic spindle localization	9	43	8.717e-06
GO:BP	GO:0040007	growth	46	929	8.928e-06
GO:BP	GO:0090306	meiotic spindle assembly	6	15	1.200e-05
GO:BP	GO:0000915	actomyosin contractile ring assembly	5	9	1.496e-05
GO:BP	GO:0000912	assembly of actomyosin apparatus involved in cytokinesis	5	9	1.496e-05
GO:BP	GO:0051054	positive regulation of DNA metabolic process	22	291	1.631e-05
GO:BP	GO:0104004	cellular response to environmental stimulus	24	339	1.657e-05
GO:BP	GO:0071214	cellular response to abiotic stimulus	24	339	1.657e-05
GO:BP	GO:1902412	regulation of mitotic cytokinesis	6	16	1.829e-05
GO:BP	GO:0045840	positive regulation of mitotic nuclear division	9	47	1.863e-05
GO:BP	GO:0048589	developmental growth	36	663	2.075e-05
GO:BP	GO:0090224	regulation of spindle organization	9	48	2.227e-05
GO:BP	GO:0048856	anatomical structure development	181	5997	2.508e-05
GO:BP	GO:0045842	positive regulation of mitotic metaphase/anaphase transition	6	17	2.709e-05
GO:BP	GO:0051307	meiotic chromosome separation	5	10	2.787e-05
GO:BP	GO:0044837	actomyosin contractile ring organization	5	10	2.787e-05
GO:BP	GO:0022616	DNA strand elongation	8	37	2.805e-05
GO:BP	GO:0032502	developmental process	194	6553	2.931e-05
GO:BP	GO:0032506	cytokinetic process	9	50	3.095e-05
GO:BP	GO:0051785	positive regulation of nuclear division	10	64	3.119e-05
GO:BP	GO:0031297	replication fork processing	9	51	3.651e-05
GO:BP	GO:1902101	positive regulation of metaphase/anaphase transition of cell cycle	6	18	3.842e-05
GO:BP	GO:0007292	female gamete generation	16	174	4.084e-05
GO:BP	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	7	28	4.468e-05
GO:BP	GO:0009411	response to UV	15	155	4.476e-05
GO:BP	GO:0050790	regulation of catalytic activity	44	928	4.579e-05
GO:BP	GO:0033314	mitotic DNA replication checkpoint signaling	5	11	4.771e-05
GO:BP	GO:0042127	regulation of cell population proliferation	67	1685	5.133e-05
GO:BP	GO:0051445	regulation of meiotic cell cycle	10	68	5.312e-05
GO:BP	GO:1901978	positive regulation of cell cycle checkpoint	6	19	5.318e-05
GO:BP	GO:0016310	phosphorylation	56	1320	5.607e-05
GO:BP	GO:0006468	protein phosphorylation	53	1227	6.307e-05
GO:BP	GO:0036297	interstrand cross-link repair	8	42	7.241e-05
GO:BP	GO:0010032	meiotic chromosome condensation	4	6	7.341e-05
GO:BP	GO:0090267	positive regulation of mitotic cell cycle spindle assembly checkpoint	5	12	7.722e-05
GO:BP	GO:0007056	spindle assembly involved in female meiosis	5	12	7.722e-05
GO:BP	GO:0048513	animal organ development	105	3085	7.862e-05
GO:BP	GO:0007275	multicellular organism development	147	4727	8.565e-05
GO:BP	GO:0071479	cellular response to ionizing radiation	10	72	8.669e-05
GO:BP	GO:1902751	positive regulation of cell cycle G2/M phase transition	7	31	8.702e-05
GO:BP	GO:0007064	mitotic sister chromatid cohesion	7	31	8.702e-05
GO:BP	GO:0007154	cell communication	191	6540	9.128e-05
GO:BP	GO:0007165	signal transduction	178	6002	9.531e-05
GO:BP	GO:0000731	DNA synthesis involved in DNA repair	8	44	9.943e-05
GO:BP	GO:0060236	regulation of mitotic spindle organization	8	44	9.943e-05
GO:BP	GO:0023052	signaling	190	6515	1.076e-04
GO:BP	GO:0007144	female meiosis I	5	13	1.177e-04
GO:BP	GO:0140527	reciprocal homologous recombination	9	60	1.318e-04
GO:BP	GO:0007131	reciprocal meiotic recombination	9	60	1.318e-04
GO:BP	GO:0048523	negative regulation of cellular process	168	5629	1.439e-04
GO:BP	GO:0051338	regulation of transferase activity	28	498	1.534e-04
GO:BP	GO:1901994	negative regulation of meiotic cell cycle phase transition	4	7	1.556e-04
GO:BP	GO:0044785	metaphase/anaphase transition of meiotic cell cycle	4	7	1.556e-04
GO:BP	GO:0090235	regulation of metaphase plate congression	5	14	1.747e-04
GO:BP	GO:0033316	meiotic spindle assembly checkpoint signaling	3	3	2.103e-04
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	10	80	2.120e-04
GO:BP	GO:0048519	negative regulation of biological process	172	5834	2.158e-04
GO:BP	GO:0006301	postreplication repair	7	36	2.343e-04
GO:BP	GO:0007276	gamete generation	39	841	2.577e-04
GO:BP	GO:0000132	establishment of mitotic spindle orientation	7	37	2.813e-04
GO:BP	GO:0009790	embryo development	48	1135	2.944e-04
GO:BP	GO:1905832	positive regulation of spindle assembly	4	8	2.951e-04
GO:BP	GO:0010332	response to gamma radiation	8	52	3.365e-04
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	14	164	3.531e-04
GO:BP	GO:0051649	establishment of localization in cell	73	2010	3.594e-04
GO:BP	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	11	105	4.127e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	71	1953	4.571e-04
GO:BP	GO:0031573	mitotic intra-S DNA damage checkpoint signaling	5	17	4.843e-04
GO:BP	GO:1902423	regulation of attachment of mitotic spindle microtubules to kinetochore	4	9	5.064e-04
GO:BP	GO:0062033	positive regulation of mitotic sister chromatid segregation	4	9	5.064e-04
GO:BP	GO:0048731	system development	126	4053	5.234e-04
GO:BP	GO:0051447	negative regulation of meiotic cell cycle	5	18	6.486e-04
GO:BP	GO:0010165	response to X-ray	6	29	6.489e-04
GO:BP	GO:0014855	striated muscle cell proliferation	9	74	6.801e-04
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	14	176	7.443e-04
GO:BP	GO:1990086	lens fiber cell apoptotic process	3	4	7.532e-04
GO:BP	GO:0003150	muscular septum morphogenesis	3	4	7.532e-04
GO:BP	GO:0007057	spindle assembly involved in female meiosis I	3	4	7.532e-04
GO:BP	GO:0044779	meiotic spindle checkpoint signaling	3	4	7.532e-04
GO:BP	GO:0043060	meiotic metaphase I homologous chromosome alignment	3	4	7.532e-04
GO:BP	GO:0033313	meiotic cell cycle checkpoint signaling	4	10	7.965e-04
GO:BP	GO:2000241	regulation of reproductive process	15	203	9.123e-04
GO:BP	GO:0071168	protein localization to chromatin	8	60	9.123e-04
GO:BP	GO:0006796	phosphate-containing compound metabolic process	82	2407	9.469e-04
GO:BP	GO:0006793	phosphorus metabolic process	82	2410	9.850e-04
GO:BP	GO:0048609	multicellular organismal reproductive process	42	1000	1.090e-03
GO:BP	GO:0006298	mismatch repair	6	32	1.113e-03
GO:BP	GO:0051053	negative regulation of DNA metabolic process	12	139	1.132e-03
GO:BP	GO:0022411	cellular component disassembly	24	446	1.178e-03
GO:BP	GO:0051987	positive regulation of attachment of spindle microtubules to kinetochore	4	11	1.191e-03
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	19	312	1.344e-03
GO:BP	GO:0010224	response to UV-B	5	21	1.357e-03
GO:BP	GO:0065009	regulation of molecular function	56	1496	1.536e-03
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	9	83	1.580e-03
GO:BP	GO:0008284	positive regulation of cell population proliferation	40	954	1.643e-03
GO:BP	GO:1905133	negative regulation of meiotic chromosome separation	3	5	1.699e-03
GO:BP	GO:1902292	cell cycle DNA replication initiation	3	5	1.699e-03
GO:BP	GO:1905784	regulation of anaphase-promoting complex-dependent catabolic process	3	5	1.699e-03
GO:BP	GO:1902315	nuclear cell cycle DNA replication initiation	3	5	1.699e-03
GO:BP	GO:0051311	meiotic metaphase chromosome alignment	3	5	1.699e-03
GO:BP	GO:1902975	mitotic DNA replication initiation	3	5	1.699e-03
GO:BP	GO:0001832	blastocyst growth	5	22	1.699e-03
GO:BP	GO:1902103	negative regulation of metaphase/anaphase transition of meiotic cell cycle	3	5	1.699e-03
GO:BP	GO:0032886	regulation of microtubule-based process	17	266	1.699e-03
GO:BP	GO:0110030	regulation of G2/MI transition of meiotic cell cycle	3	5	1.699e-03
GO:BP	GO:1902410	mitotic cytokinetic process	6	35	1.766e-03
GO:BP	GO:0007019	microtubule depolymerization	7	50	1.800e-03
GO:BP	GO:0007548	sex differentiation	18	294	1.818e-03
GO:BP	GO:0009966	regulation of signal transduction	97	3034	1.854e-03
GO:BP	GO:0051641	cellular localization	113	3661	1.874e-03
GO:BP	GO:0051347	positive regulation of transferase activity	18	296	1.960e-03
GO:BP	GO:0009416	response to light stimulus	19	323	1.973e-03
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	7	51	2.001e-03
GO:BP	GO:0045910	negative regulation of DNA recombination	7	51	2.001e-03
GO:BP	GO:0043085	positive regulation of catalytic activity	27	554	2.048e-03
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	12	150	2.143e-03
GO:BP	GO:0023051	regulation of signaling	108	3478	2.153e-03
GO:BP	GO:0008584	male gonad development	12	152	2.413e-03
GO:BP	GO:0048144	fibroblast proliferation	10	109	2.482e-03
GO:BP	GO:0046661	male sex differentiation	13	176	2.521e-03
GO:BP	GO:0046546	development of primary male sexual characteristics	12	153	2.543e-03
GO:BP	GO:0034644	cellular response to UV	9	90	2.702e-03
GO:BP	GO:0048146	positive regulation of fibroblast proliferation	7	54	2.810e-03
GO:BP	GO:0060045	positive regulation of cardiac muscle cell proliferation	5	25	2.967e-03
GO:BP	GO:2000105	positive regulation of DNA-templated DNA replication	4	14	3.001e-03
GO:BP	GO:0046385	deoxyribose phosphate biosynthetic process	4	14	3.001e-03
GO:BP	GO:0001833	inner cell mass cell proliferation	4	14	3.001e-03
GO:BP	GO:1900025	negative regulation of substrate adhesion-dependent cell spreading	4	14	3.001e-03
GO:BP	GO:0009263	deoxyribonucleotide biosynthetic process	4	14	3.001e-03
GO:BP	GO:0009265	2’-deoxyribonucleotide biosynthetic process	4	14	3.001e-03
GO:BP	GO:0036211	protein modification process	91	2846	3.001e-03
GO:BP	GO:0003175	tricuspid valve development	3	6	3.033e-03
GO:BP	GO:1905132	regulation of meiotic chromosome separation	3	6	3.033e-03
GO:BP	GO:0006335	DNA replication-dependent chromatin assembly	3	6	3.033e-03
GO:BP	GO:0016321	female meiosis chromosome segregation	3	6	3.033e-03
GO:BP	GO:1902102	regulation of metaphase/anaphase transition of meiotic cell cycle	3	6	3.033e-03
GO:BP	GO:0048583	regulation of response to stimulus	120	3993	3.058e-03
GO:BP	GO:0030154	cell differentiation	131	4437	3.058e-03
GO:BP	GO:0048869	cellular developmental process	131	4438	3.080e-03
GO:BP	GO:0048638	regulation of developmental growth	18	310	3.176e-03
GO:BP	GO:0040008	regulation of growth	28	604	3.266e-03
GO:BP	GO:0051298	centrosome duplication	8	74	3.379e-03
GO:BP	GO:0010646	regulation of cell communication	107	3486	3.384e-03
GO:BP	GO:0030010	establishment of cell polarity	12	159	3.388e-03
GO:BP	GO:0019985	translesion synthesis	5	26	3.388e-03
GO:BP	GO:0048608	reproductive structure development	18	314	3.648e-03
GO:BP	GO:0031109	microtubule polymerization or depolymerization	11	138	3.789e-03
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	7	58	4.101e-03
GO:BP	GO:0061458	reproductive system development	18	318	4.215e-03
GO:BP	GO:0008406	gonad development	15	238	4.284e-03
GO:BP	GO:0007099	centriole replication	6	43	4.932e-03
GO:BP	GO:0051782	negative regulation of cell division	4	16	4.932e-03
GO:BP	GO:0045740	positive regulation of DNA replication	6	43	4.932e-03
GO:BP	GO:0051299	centrosome separation	4	16	4.932e-03
GO:BP	GO:0045137	development of primary sexual characteristics	15	243	5.266e-03
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	7	61	5.478e-03
GO:BP	GO:0007420	brain development	32	754	5.478e-03
GO:BP	GO:0055023	positive regulation of cardiac muscle tissue growth	5	29	5.576e-03
GO:BP	GO:0006338	chromatin remodeling	31	725	5.899e-03
GO:BP	GO:0044380	protein localization to cytoskeleton	7	62	6.008e-03
GO:BP	GO:0006915	apoptotic process	65	1923	6.055e-03
GO:BP	GO:0046622	positive regulation of organ growth	6	45	6.189e-03
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	6	45	6.189e-03
GO:BP	GO:1905325	regulation of meiosis I spindle assembly checkpoint	2	2	6.462e-03
GO:BP	GO:0031619	homologous chromosome orientation in meiotic metaphase I	2	2	6.462e-03
GO:BP	GO:1905318	meiosis I spindle assembly checkpoint signaling	2	2	6.462e-03
GO:BP	GO:0141112	broken chromosome clustering	2	2	6.462e-03
GO:BP	GO:1990426	mitotic recombination-dependent replication fork processing	2	2	6.462e-03
GO:BP	GO:0099607	lateral attachment of mitotic spindle microtubules to kinetochore	2	2	6.462e-03
GO:BP	GO:0110029	negative regulation of meiosis I	2	2	6.462e-03
GO:BP	GO:1990505	mitotic DNA replication maintenance of fidelity	2	2	6.462e-03
GO:BP	GO:1902298	cell cycle DNA replication maintenance of fidelity	2	2	6.462e-03
GO:BP	GO:0140274	repair of kinetochore microtubule attachment defect	2	2	6.462e-03
GO:BP	GO:0140273	repair of mitotic kinetochore microtubule attachment defect	2	2	6.462e-03
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	7	64	7.012e-03
GO:BP	GO:0007077	mitotic nuclear membrane disassembly	3	8	7.261e-03
GO:BP	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	3	8	7.261e-03
GO:BP	GO:0010458	exit from mitosis	5	31	7.261e-03
GO:BP	GO:1902425	positive regulation of attachment of mitotic spindle microtubules to kinetochore	3	8	7.261e-03
GO:BP	GO:0097681	double-strand break repair via alternative nonhomologous end joining	3	8	7.261e-03
GO:BP	GO:0007096	regulation of exit from mitosis	4	18	7.423e-03
GO:BP	GO:0060322	head development	33	806	7.781e-03
GO:BP	GO:0098534	centriole assembly	6	48	8.354e-03
GO:BP	GO:0045777	positive regulation of blood pressure	5	33	9.579e-03
GO:BP	GO:0006325	chromatin organization	35	884	9.579e-03
GO:BP	GO:0060421	positive regulation of heart growth	5	33	9.579e-03
GO:BP	GO:0051642	centrosome localization	5	33	9.579e-03
GO:BP	GO:0061842	microtubule organizing center localization	5	33	9.579e-03
GO:BP	GO:0007163	establishment or maintenance of cell polarity	14	234	1.011e-02
GO:BP	GO:0060038	cardiac muscle cell proliferation	6	50	1.023e-02
GO:BP	GO:1904776	regulation of protein localization to cell cortex	3	9	1.036e-02
GO:BP	GO:0046601	positive regulation of centriole replication	3	9	1.036e-02
GO:BP	GO:0043653	mitochondrial fragmentation involved in apoptotic process	3	9	1.036e-02
GO:BP	GO:0090169	regulation of spindle assembly	5	34	1.083e-02
GO:BP	GO:1904666	regulation of ubiquitin protein ligase activity	4	20	1.094e-02
GO:BP	GO:0048145	regulation of fibroblast proliferation	8	90	1.102e-02
GO:BP	GO:0040020	regulation of meiotic nuclear division	5	35	1.232e-02
GO:BP	GO:0043412	macromolecule modification	92	3030	1.261e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	8	92	1.262e-02
GO:BP	GO:0001701	in utero embryonic development	20	413	1.262e-02
GO:BP	GO:0012501	programmed cell death	65	1987	1.276e-02
GO:BP	GO:0008219	cell death	65	1991	1.339e-02
GO:BP	GO:0072331	signal transduction by p53 class mediator	11	164	1.389e-02
GO:BP	GO:0035265	organ growth	11	164	1.389e-02
GO:BP	GO:1904668	positive regulation of ubiquitin protein ligase activity	3	10	1.408e-02
GO:BP	GO:0045835	negative regulation of meiotic nuclear division	3	10	1.408e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	29	706	1.469e-02
GO:BP	GO:0007129	homologous chromosome pairing at meiosis	6	54	1.475e-02
GO:BP	GO:2000242	negative regulation of reproductive process	7	74	1.537e-02
GO:BP	GO:2000001	regulation of DNA damage checkpoint	4	22	1.537e-02
GO:BP	GO:1903475	mitotic actomyosin contractile ring assembly	2	3	1.713e-02
GO:BP	GO:1903479	mitotic actomyosin contractile ring assembly actin filament organization	2	3	1.713e-02
GO:BP	GO:0110032	positive regulation of G2/MI transition of meiotic cell cycle	2	3	1.713e-02
GO:BP	GO:1902407	assembly of actomyosin apparatus involved in mitotic cytokinesis	2	3	1.713e-02
GO:BP	GO:0000018	regulation of DNA recombination	10	144	1.713e-02
GO:BP	GO:0034421	post-translational protein acetylation	2	3	1.713e-02
GO:BP	GO:0060043	regulation of cardiac muscle cell proliferation	5	38	1.713e-02
GO:BP	GO:0071163	DNA replication preinitiation complex assembly	2	3	1.713e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	56	1.740e-02
GO:BP	GO:0060392	negative regulation of SMAD protein signal transduction	4	23	1.780e-02
GO:BP	GO:0046599	regulation of centriole replication	4	23	1.780e-02
GO:BP	GO:0051261	protein depolymerization	9	121	1.802e-02
GO:BP	GO:0048585	negative regulation of response to stimulus	56	1680	1.804e-02
GO:BP	GO:1990918	double-strand break repair involved in meiotic recombination	3	11	1.811e-02
GO:BP	GO:0072711	cellular response to hydroxyurea	3	11	1.811e-02
GO:BP	GO:0072697	protein localization to cell cortex	3	11	1.811e-02
GO:BP	GO:0070601	centromeric sister chromatid cohesion	3	11	1.811e-02
GO:BP	GO:0048468	cell development	87	2876	1.839e-02
GO:BP	GO:0071482	cellular response to light stimulus	9	122	1.876e-02
GO:BP	GO:0033365	protein localization to organelle	43	1209	1.918e-02
GO:BP	GO:0009162	deoxyribonucleoside monophosphate metabolic process	4	24	2.050e-02
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	28	692	2.078e-02
GO:BP	GO:0003006	developmental process involved in reproduction	38	1038	2.139e-02
GO:BP	GO:0031099	regeneration	12	202	2.222e-02
GO:BP	GO:0072710	response to hydroxyurea	3	12	2.305e-02
GO:BP	GO:0003203	endocardial cushion morphogenesis	5	41	2.305e-02
GO:BP	GO:0071493	cellular response to UV-B	3	12	2.305e-02
GO:BP	GO:0051081	nuclear membrane disassembly	3	12	2.305e-02
GO:BP	GO:0009394	2’-deoxyribonucleotide metabolic process	5	41	2.305e-02
GO:BP	GO:0042276	error-prone translesion synthesis	3	12	2.305e-02
GO:BP	GO:0001783	B cell apoptotic process	4	25	2.333e-02
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	4	25	2.333e-02
GO:BP	GO:0006312	mitotic recombination	4	25	2.333e-02
GO:BP	GO:0060420	regulation of heart growth	6	60	2.349e-02
GO:BP	GO:0048678	response to axon injury	7	81	2.383e-02
GO:BP	GO:0060395	SMAD protein signal transduction	7	81	2.383e-02
GO:BP	GO:0003231	cardiac ventricle development	9	127	2.383e-02
GO:BP	GO:0050673	epithelial cell proliferation	20	441	2.444e-02
GO:BP	GO:0009262	deoxyribonucleotide metabolic process	5	42	2.506e-02
GO:BP	GO:0019692	deoxyribose phosphate metabolic process	5	42	2.506e-02
GO:BP	GO:0043009	chordate embryonic development	27	671	2.576e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	4	26	2.643e-02
GO:BP	GO:0062009	secondary palate development	4	26	2.643e-02
GO:BP	GO:0008156	negative regulation of DNA replication	4	26	2.643e-02
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	7	83	2.686e-02
GO:BP	GO:0060419	heart growth	7	83	2.686e-02
GO:BP	GO:0002262	myeloid cell homeostasis	11	181	2.686e-02
GO:BP	GO:0032147	activation of protein kinase activity	6	62	2.694e-02
GO:BP	GO:0030866	cortical actin cytoskeleton organization	5	43	2.730e-02
GO:BP	GO:0051179	localization	151	5555	2.737e-02
GO:BP	GO:0060429	epithelium development	43	1238	2.779e-02
GO:BP	GO:0040015	negative regulation of multicellular organism growth	3	13	2.782e-02
GO:BP	GO:1903251	multi-ciliated epithelial cell differentiation	3	13	2.782e-02
GO:BP	GO:0016446	somatic hypermutation of immunoglobulin genes	3	13	2.782e-02
GO:BP	GO:0030397	membrane disassembly	3	13	2.782e-02
GO:BP	GO:0070914	UV-damage excision repair	3	13	2.782e-02
GO:BP	GO:0007417	central nervous system development	38	1061	2.885e-02
GO:BP	GO:0050793	regulation of developmental process	75	2457	2.912e-02
GO:BP	GO:0071480	cellular response to gamma radiation	4	27	2.918e-02
GO:BP	GO:0002339	B cell selection	2	4	2.918e-02
GO:BP	GO:1905007	positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation	2	4	2.918e-02
GO:BP	GO:2000689	actomyosin contractile ring assembly actin filament organization	2	4	2.918e-02
GO:BP	GO:1905448	positive regulation of mitochondrial ATP synthesis coupled electron transport	2	4	2.918e-02
GO:BP	GO:0072757	cellular response to camptothecin	2	4	2.918e-02
GO:BP	GO:0051296	establishment of meiotic spindle orientation	2	4	2.918e-02
GO:BP	GO:1905005	regulation of epithelial to mesenchymal transition involved in endocardial cushion formation	2	4	2.918e-02
GO:BP	GO:1901995	positive regulation of meiotic cell cycle phase transition	2	4	2.918e-02
GO:BP	GO:1901563	response to camptothecin	2	4	2.918e-02
GO:BP	GO:0048627	myoblast development	2	4	2.918e-02
GO:BP	GO:0007079	mitotic chromosome movement towards spindle pole	2	4	2.918e-02
GO:BP	GO:0051754	meiotic sister chromatid cohesion, centromeric	2	4	2.918e-02
GO:BP	GO:0060400	negative regulation of growth hormone receptor signaling pathway	2	4	2.918e-02
GO:BP	GO:0051493	regulation of cytoskeleton organization	22	517	3.056e-02
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	11	186	3.128e-02
GO:BP	GO:0023057	negative regulation of signaling	48	1435	3.181e-02
GO:BP	GO:0080135	regulation of cellular response to stress	22	519	3.181e-02
GO:BP	GO:0035264	multicellular organism growth	10	160	3.187e-02
GO:BP	GO:0010648	negative regulation of cell communication	48	1436	3.204e-02
GO:BP	GO:0003272	endocardial cushion formation	4	28	3.238e-02
GO:BP	GO:0009968	negative regulation of signal transduction	45	1326	3.238e-02
GO:BP	GO:0033262	regulation of nuclear cell cycle DNA replication	3	14	3.285e-02
GO:BP	GO:0007100	mitotic centrosome separation	3	14	3.285e-02
GO:BP	GO:0051177	meiotic sister chromatid cohesion	3	14	3.285e-02
GO:BP	GO:0002566	somatic diversification of immune receptors via somatic mutation	3	14	3.285e-02
GO:BP	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	5	46	3.413e-02
GO:BP	GO:0050678	regulation of epithelial cell proliferation	17	364	3.414e-02
GO:BP	GO:0009987	cellular process	461	20247	3.540e-02
GO:BP	GO:0042325	regulation of phosphorylation	31	830	3.552e-02
GO:BP	GO:0046620	regulation of organ growth	7	89	3.636e-02
GO:BP	GO:0001947	heart looping	6	67	3.647e-02
GO:BP	GO:0007399	nervous system development	78	2604	3.647e-02
GO:BP	GO:0000723	telomere maintenance	10	164	3.680e-02
GO:BP	GO:0048639	positive regulation of developmental growth	10	164	3.680e-02
GO:BP	GO:0043549	regulation of kinase activity	19	431	3.763e-02
GO:BP	GO:2000243	positive regulation of reproductive process	7	90	3.823e-02
GO:BP	GO:0031100	animal organ regeneration	6	68	3.884e-02
GO:BP	GO:0003198	epithelial to mesenchymal transition involved in endocardial cushion formation	3	15	3.919e-02
GO:BP	GO:0044027	negative regulation of gene expression via chromosomal CpG island methylation	3	15	3.919e-02
GO:BP	GO:0009130	pyrimidine nucleoside monophosphate biosynthetic process	3	15	3.919e-02
GO:BP	GO:0051094	positive regulation of developmental process	45	1343	3.921e-02
GO:BP	GO:0045859	regulation of protein kinase activity	18	402	3.972e-02
GO:BP	GO:0071763	nuclear membrane organization	5	48	3.975e-02
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	8	115	4.015e-02
GO:BP	GO:0060411	cardiac septum morphogenesis	6	69	4.110e-02
GO:BP	GO:0009888	tissue development	63	2032	4.162e-02
GO:BP	GO:0045666	positive regulation of neuron differentiation	7	92	4.225e-02
GO:BP	GO:0071962	mitotic sister chromatid cohesion, centromeric	2	5	4.361e-02
GO:BP	GO:0098535	de novo centriole assembly involved in multi-ciliated epithelial cell differentiation	2	5	4.361e-02
GO:BP	GO:0098722	asymmetric stem cell division	2	5	4.361e-02
GO:BP	GO:0098728	germline stem cell asymmetric division	2	5	4.361e-02
GO:BP	GO:0090233	negative regulation of spindle checkpoint	2	5	4.361e-02
GO:BP	GO:0003186	tricuspid valve morphogenesis	2	5	4.361e-02
GO:BP	GO:0003208	cardiac ventricle morphogenesis	6	70	4.361e-02
GO:BP	GO:0140499	negative regulation of mitotic spindle assembly checkpoint signaling	2	5	4.361e-02
GO:BP	GO:0006297	nucleotide-excision repair, DNA gap filling	2	5	4.361e-02
GO:BP	GO:0006282	regulation of DNA repair	12	225	4.361e-02
GO:BP	GO:0031536	positive regulation of exit from mitosis	2	5	4.361e-02
GO:BP	GO:0043137	DNA replication, removal of RNA primer	2	5	4.361e-02
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	6	70	4.361e-02
GO:BP	GO:0003274	endocardial cushion fusion	2	5	4.361e-02
GO:BP	GO:2000779	regulation of double-strand break repair	9	143	4.411e-02
GO:BP	GO:0007507	heart development	24	605	4.436e-02
GO:BP	GO:1990166	protein localization to site of double-strand break	3	16	4.497e-02
GO:BP	GO:0048308	organelle inheritance	3	16	4.497e-02
GO:BP	GO:0048313	Golgi inheritance	3	16	4.497e-02
GO:BP	GO:0006334	nucleosome assembly	8	118	4.497e-02
GO:BP	GO:0003214	cardiac left ventricle morphogenesis	3	16	4.497e-02
GO:BP	GO:0044093	positive regulation of molecular function	32	884	4.522e-02
GO:BP	GO:0061351	neural precursor cell proliferation	10	171	4.604e-02
GO:BP	GO:0001824	blastocyst development	8	119	4.685e-02
GO:BP	GO:0032984	protein-containing complex disassembly	13	257	4.712e-02
GO:BP	GO:0048640	negative regulation of developmental growth	7	95	4.785e-02
GO:BP	GO:1904376	negative regulation of protein localization to cell periphery	4	32	4.785e-02
GO:BP	GO:0007018	microtubule-based movement	20	478	4.933e-02
KEGG	KEGG:04110	Cell cycle	45	157	6.713e-33
KEGG	KEGG:03030	DNA replication	17	36	4.517e-16
KEGG	KEGG:04115	p53 signaling pathway	14	74	4.224e-07
KEGG	KEGG:03460	Fanconi anemia pathway	12	54	5.928e-07
KEGG	KEGG:04114	Oocyte meiosis	17	131	2.176e-06
KEGG	KEGG:03440	Homologous recombination	10	41	2.687e-06
KEGG	KEGG:03430	Mismatch repair	7	23	4.458e-05
KEGG	KEGG:04914	Progesterone-mediated oocyte maturation	12	102	3.428e-04
KEGG	KEGG:04218	Cellular senescence	15	155	3.428e-04
KEGG	KEGG:03410	Base excision repair	8	44	3.627e-04
KEGG	KEGG:05212	Pancreatic cancer	10	76	5.152e-04
KEGG	KEGG:03420	Nucleotide excision repair	9	61	5.152e-04
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	17	218	9.973e-04
KEGG	KEGG:04814	Motor proteins	15	193	2.657e-03
KEGG	KEGG:05222	Small cell lung cancer	9	92	1.024e-02
KEGG	KEGG:05220	Chronic myeloid leukemia	8	76	1.176e-02
KEGG	KEGG:04934	Cushing syndrome	11	153	3.091e-02
KEGG	KEGG:01524	Platinum drug resistance	7	72	3.329e-02
KEGG	KEGG:05223	Non-small cell lung cancer	7	72	3.329e-02
KEGG	KEGG:05214	Glioma	7	75	3.990e-02

#GO:BP
table_DOX144Rshare_genes_GOBP <- table_DOX144Rshare_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX144Rshare_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX144R Shared DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-11.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX144Rshare_genes_KEGG <- table_DOX144Rshare_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX144Rshare_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX144R Shared DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "GO KEGG Overlap DEGs Original-12.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###GO/KEGG Analysis of Upreg and Downreg Genes Original Data

# library(gprofiler2)
#####DOX24 Upregulated Genes#####
D24_DEGs_up_mat <- as.matrix(DOX24T_DEGs_GO_up)

DOX_24_up_dxr_gene <- gost(query = D24_DEGs_up_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24_up_gost_genes <- gostplot(DOX_24_up_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24_up_gost_genes

table_DOX24_up_genes <- DOX_24_up_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24_up_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	576	5390	1.045e-15
GO:BP	GO:0019538	protein metabolic process	506	4721	2.272e-13
GO:BP	GO:0048518	positive regulation of biological process	634	6264	6.684e-13
GO:BP	GO:0048522	positive regulation of cellular process	604	5920	6.884e-13
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	438	3990	6.884e-13
GO:BP	GO:0065007	biological regulation	1136	12743	3.199e-12
GO:BP	GO:0050789	regulation of biological process	1104	12336	6.167e-12
GO:BP	GO:0051252	regulation of RNA metabolic process	405	3687	7.025e-12
GO:BP	GO:0050794	regulation of cellular process	1074	11946	7.025e-12
GO:BP	GO:0036211	protein modification process	319	2846	1.022e-09
GO:BP	GO:0023051	regulation of signaling	374	3478	1.999e-09
GO:BP	GO:0006355	regulation of DNA-templated transcription	366	3409	4.296e-09
GO:BP	GO:0007275	multicellular organism development	480	4727	4.661e-09
GO:BP	GO:0010646	regulation of cell communication	372	3486	4.904e-09
GO:BP	GO:2001141	regulation of RNA biosynthetic process	367	3428	4.904e-09
GO:BP	GO:0009056	catabolic process	296	2639	4.904e-09
GO:BP	GO:0043412	macromolecule modification	331	3030	5.358e-09
GO:BP	GO:0048583	regulation of response to stimulus	415	3993	7.293e-09
GO:BP	GO:0051716	cellular response to stimulus	697	7376	7.338e-09
GO:BP	GO:0035556	intracellular signal transduction	324	2965	7.338e-09
GO:BP	GO:0006351	DNA-templated transcription	376	3549	7.338e-09
GO:BP	GO:0051253	negative regulation of RNA metabolic process	178	1400	7.338e-09
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	190	1529	9.567e-09
GO:BP	GO:0032502	developmental process	629	6553	9.602e-09
GO:BP	GO:0048856	anatomical structure development	583	5997	9.625e-09
GO:BP	GO:0050793	regulation of developmental process	277	2457	9.625e-09
GO:BP	GO:0048523	negative regulation of cellular process	550	5629	2.235e-08
GO:BP	GO:0009966	regulation of signal transduction	327	3034	2.335e-08
GO:BP	GO:0009968	negative regulation of signal transduction	168	1326	2.744e-08
GO:BP	GO:0048585	negative regulation of response to stimulus	201	1680	5.285e-08
GO:BP	GO:0023057	negative regulation of signaling	177	1435	6.564e-08
GO:BP	GO:0019222	regulation of metabolic process	662	7035	6.564e-08
GO:BP	GO:0051179	localization	540	5555	7.321e-08
GO:BP	GO:0006810	transport	443	4407	7.975e-08
GO:BP	GO:0010648	negative regulation of cell communication	176	1436	1.111e-07
GO:BP	GO:0048519	negative regulation of biological process	561	5834	1.428e-07
GO:BP	GO:0006796	phosphate-containing compound metabolic process	264	2407	3.563e-07
GO:BP	GO:0023052	signaling	614	6515	3.674e-07
GO:BP	GO:0006793	phosphorus metabolic process	264	2410	3.819e-07
GO:BP	GO:0048731	system development	408	4053	4.044e-07
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	158	1280	4.890e-07
GO:BP	GO:0007154	cell communication	614	6540	6.087e-07
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	159	1296	6.087e-07
GO:BP	GO:0050896	response to stimulus	811	8999	6.087e-07
GO:BP	GO:0035295	tube development	140	1101	6.087e-07
GO:BP	GO:0006325	chromatin organization	118	884	6.705e-07
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	277	2578	7.967e-07
GO:BP	GO:0007166	cell surface receptor signaling pathway	298	2819	9.410e-07
GO:BP	GO:0046907	intracellular transport	166	1381	1.072e-06
GO:BP	GO:0044281	small molecule metabolic process	203	1776	1.157e-06
GO:BP	GO:0033554	cellular response to stress	208	1830	1.157e-06
GO:BP	GO:0030154	cell differentiation	437	4437	1.180e-06
GO:BP	GO:0048869	cellular developmental process	437	4438	1.193e-06
GO:BP	GO:0009893	positive regulation of metabolic process	365	3597	1.233e-06
GO:BP	GO:0006366	transcription by RNA polymerase II	287	2711	1.478e-06
GO:BP	GO:0007165	signal transduction	566	6002	1.729e-06
GO:BP	GO:0032879	regulation of localization	224	2029	2.987e-06
GO:BP	GO:0043687	post-translational protein modification	129	1027	4.072e-06
GO:BP	GO:0051641	cellular localization	367	3661	4.085e-06
GO:BP	GO:0042592	homeostatic process	196	1736	4.749e-06
GO:BP	GO:0016055	Wnt signaling pathway	70	458	4.826e-06
GO:BP	GO:0033036	macromolecule localization	329	3228	4.873e-06
GO:BP	GO:0032446	protein modification by small protein conjugation	111	853	5.512e-06
GO:BP	GO:0051234	establishment of localization	473	4928	5.512e-06
GO:BP	GO:0060562	epithelial tube morphogenesis	56	336	5.512e-06
GO:BP	GO:0048762	mesenchymal cell differentiation	46	252	5.512e-06
GO:BP	GO:0060070	canonical Wnt signaling pathway	53	311	5.778e-06
GO:BP	GO:0060485	mesenchyme development	54	320	5.986e-06
GO:BP	GO:0009653	anatomical structure morphogenesis	283	2713	6.310e-06
GO:BP	GO:0051239	regulation of multicellular organismal process	304	2956	7.053e-06
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	122	975	9.981e-06
GO:BP	GO:0060255	regulation of macromolecule metabolic process	599	6492	1.141e-05
GO:BP	GO:0001837	epithelial to mesenchymal transition	35	171	1.141e-05
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	118	938	1.181e-05
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	220	2036	1.694e-05
GO:BP	GO:0030111	regulation of Wnt signaling pathway	54	331	1.694e-05
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	45	255	1.831e-05
GO:BP	GO:0032880	regulation of protein localization	114	907	1.945e-05
GO:BP	GO:0009889	regulation of biosynthetic process	541	5809	2.022e-05
GO:BP	GO:0016567	protein ubiquitination	100	768	2.099e-05
GO:BP	GO:0035239	tube morphogenesis	111	879	2.152e-05
GO:BP	GO:0048468	cell development	293	2876	2.683e-05
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	57	364	2.898e-05
GO:BP	GO:0061053	somite development	22	85	3.606e-05
GO:BP	GO:0060341	regulation of cellular localization	123	1013	3.797e-05
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	31	150	4.104e-05
GO:BP	GO:2000026	regulation of multicellular organismal development	161	1418	4.417e-05
GO:BP	GO:0061013	regulation of mRNA catabolic process	37	198	4.628e-05
GO:BP	GO:0035282	segmentation	25	108	5.614e-05
GO:BP	GO:0071495	cellular response to endogenous stimulus	142	1223	6.125e-05
GO:BP	GO:0006996	organelle organization	352	3594	6.328e-05
GO:BP	GO:0051649	establishment of localization in cell	214	2010	6.369e-05
GO:BP	GO:0009892	negative regulation of metabolic process	333	3375	6.859e-05
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	23	96	7.805e-05
GO:BP	GO:0045595	regulation of cell differentiation	174	1576	8.306e-05
GO:BP	GO:0032501	multicellular organismal process	657	7322	1.020e-04
GO:BP	GO:0009891	positive regulation of biosynthetic process	273	2696	1.074e-04
GO:BP	GO:0043009	chordate embryonic development	87	671	1.279e-04
GO:BP	GO:0009790	embryo development	132	1135	1.290e-04
GO:BP	GO:0009057	macromolecule catabolic process	158	1417	1.431e-04
GO:BP	GO:0051254	positive regulation of RNA metabolic process	196	1835	1.431e-04
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	44	268	1.431e-04
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	323	3288	1.431e-04
GO:BP	GO:0006950	response to stress	379	3948	1.431e-04
GO:BP	GO:0065009	regulation of molecular function	165	1496	1.557e-04
GO:BP	GO:0019637	organophosphate metabolic process	126	1077	1.557e-04
GO:BP	GO:0008104	protein localization	278	2770	1.600e-04
GO:BP	GO:0051049	regulation of transport	175	1607	1.612e-04
GO:BP	GO:0071705	nitrogen compound transport	203	1923	1.936e-04
GO:BP	GO:0048598	embryonic morphogenesis	81	620	1.947e-04
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	52	344	2.085e-04
GO:BP	GO:0070727	cellular macromolecule localization	278	2782	2.177e-04
GO:BP	GO:0051094	positive regulation of developmental process	150	1343	2.202e-04
GO:BP	GO:0019752	carboxylic acid metabolic process	107	887	2.234e-04
GO:BP	GO:0060429	epithelium development	140	1238	2.433e-04
GO:BP	GO:0044238	primary metabolic process	1044	12342	2.433e-04
GO:BP	GO:0006338	chromatin remodeling	91	725	2.434e-04
GO:BP	GO:0043488	regulation of mRNA stability	33	181	2.468e-04
GO:BP	GO:0009719	response to endogenous stimulus	163	1489	2.494e-04
GO:BP	GO:0008219	cell death	208	1991	2.647e-04
GO:BP	GO:0030097	hemopoiesis	115	976	2.773e-04
GO:BP	GO:0090181	regulation of cholesterol metabolic process	13	39	2.963e-04
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	516	5644	3.176e-04
GO:BP	GO:0012501	programmed cell death	207	1987	3.271e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	87	692	3.366e-04
GO:BP	GO:0015031	protein transport	158	1444	3.366e-04
GO:BP	GO:0051128	regulation of cellular component organization	246	2433	3.366e-04
GO:BP	GO:0072175	epithelial tube formation	27	136	3.366e-04
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	260	2593	3.366e-04
GO:BP	GO:0002009	morphogenesis of an epithelium	68	503	3.366e-04
GO:BP	GO:0043436	oxoacid metabolic process	108	909	3.491e-04
GO:BP	GO:0051169	nuclear transport	50	334	3.524e-04
GO:BP	GO:0002320	lymphoid progenitor cell differentiation	10	24	3.524e-04
GO:BP	GO:0006913	nucleocytoplasmic transport	50	334	3.524e-04
GO:BP	GO:0009894	regulation of catabolic process	120	1040	4.203e-04
GO:BP	GO:0034504	protein localization to nucleus	48	318	4.227e-04
GO:BP	GO:0070201	regulation of establishment of protein localization	71	537	4.242e-04
GO:BP	GO:0009888	tissue development	210	2032	4.242e-04
GO:BP	GO:0006082	organic acid metabolic process	108	915	4.416e-04
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	113	970	4.875e-04
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	48	320	4.875e-04
GO:BP	GO:0006629	lipid metabolic process	152	1391	5.029e-04
GO:BP	GO:1903311	regulation of mRNA metabolic process	47	312	5.271e-04
GO:BP	GO:0035148	tube formation	28	148	5.281e-04
GO:BP	GO:0019218	regulation of steroid metabolic process	22	102	5.487e-04
GO:BP	GO:1905456	regulation of lymphoid progenitor cell differentiation	7	12	5.488e-04
GO:BP	GO:0070887	cellular response to chemical stimulus	223	2192	5.863e-04
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	306	3157	6.253e-04
GO:BP	GO:0006606	protein import into nucleus	30	166	6.402e-04
GO:BP	GO:0051093	negative regulation of developmental process	108	925	6.603e-04
GO:BP	GO:0006402	mRNA catabolic process	41	261	6.639e-04
GO:BP	GO:0009890	negative regulation of biosynthetic process	276	2813	7.378e-04
GO:BP	GO:0043487	regulation of RNA stability	33	193	7.803e-04
GO:BP	GO:0046649	lymphocyte activation	97	814	7.938e-04
GO:BP	GO:0016125	sterol metabolic process	29	160	8.084e-04
GO:BP	GO:0048584	positive regulation of response to stimulus	234	2331	8.154e-04
GO:BP	GO:0010468	regulation of gene expression	502	5536	9.334e-04
GO:BP	GO:0008203	cholesterol metabolic process	27	145	9.334e-04
GO:BP	GO:1901701	cellular response to oxygen-containing compound	131	1182	9.938e-04
GO:BP	GO:0048729	tissue morphogenesis	77	614	1.032e-03
GO:BP	GO:0006886	intracellular protein transport	84	686	1.062e-03
GO:BP	GO:0051170	import into nucleus	30	171	1.071e-03
GO:BP	GO:0065008	regulation of biological quality	286	2947	1.080e-03
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	22	107	1.080e-03
GO:BP	GO:0051248	negative regulation of protein metabolic process	83	677	1.108e-03
GO:BP	GO:0001838	embryonic epithelial tube formation	24	123	1.151e-03
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	177	1697	1.191e-03
GO:BP	GO:0072359	circulatory system development	127	1145	1.220e-03
GO:BP	GO:0016310	phosphorylation	143	1320	1.224e-03
GO:BP	GO:1902652	secondary alcohol metabolic process	28	156	1.237e-03
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	177	1699	1.244e-03
GO:BP	GO:0007399	nervous system development	256	2604	1.246e-03
GO:BP	GO:0006468	protein phosphorylation	134	1227	1.486e-03
GO:BP	GO:0006915	apoptotic process	196	1923	1.614e-03
GO:BP	GO:0060412	ventricular septum morphogenesis	12	40	1.614e-03
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	26	142	1.614e-03
GO:BP	GO:0098727	maintenance of cell number	31	184	1.620e-03
GO:BP	GO:0141124	intracellular signaling cassette	195	1912	1.620e-03
GO:BP	GO:0048732	gland development	60	454	1.658e-03
GO:BP	GO:1901699	cellular response to nitrogen compound	79	645	1.658e-03
GO:BP	GO:0001756	somitogenesis	16	67	1.915e-03
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	27	152	1.935e-03
GO:BP	GO:0007219	Notch signaling pathway	31	186	1.952e-03
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	26	144	1.978e-03
GO:BP	GO:0001568	blood vessel development	87	732	1.996e-03
GO:BP	GO:0030163	protein catabolic process	115	1030	2.027e-03
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	26	145	2.199e-03
GO:BP	GO:0080135	regulation of cellular response to stress	66	519	2.212e-03
GO:BP	GO:0007369	gastrulation	32	197	2.402e-03
GO:BP	GO:0080134	regulation of response to stress	147	1387	2.492e-03
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	21	106	2.523e-03
GO:BP	GO:0022008	neurogenesis	181	1771	2.604e-03
GO:BP	GO:1901700	response to oxygen-containing compound	172	1669	2.604e-03
GO:BP	GO:0044092	negative regulation of molecular function	69	553	2.656e-03
GO:BP	GO:0002476	antigen processing and presentation of endogenous peptide antigen via MHC class Ib	7	15	2.696e-03
GO:BP	GO:0002484	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway	7	15	2.696e-03
GO:BP	GO:0023056	positive regulation of signaling	183	1796	2.736e-03
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	39	262	2.791e-03
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	33	208	2.832e-03
GO:BP	GO:0001944	vasculature development	89	762	2.855e-03
GO:BP	GO:0051246	regulation of protein metabolic process	188	1855	2.855e-03
GO:BP	GO:0046890	regulation of lipid biosynthetic process	30	182	2.880e-03
GO:BP	GO:0009880	embryonic pattern specification	17	77	2.894e-03
GO:BP	GO:1904238	pericyte cell differentiation	6	11	2.984e-03
GO:BP	GO:0019216	regulation of lipid metabolic process	45	320	3.140e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	171	1667	3.267e-03
GO:BP	GO:0001775	cell activation	123	1132	3.295e-03
GO:BP	GO:1902531	regulation of intracellular signal transduction	196	1953	3.344e-03
GO:BP	GO:0006639	acylglycerol metabolic process	24	133	3.409e-03
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	264	2745	3.476e-03
GO:BP	GO:1901135	carbohydrate derivative metabolic process	109	983	3.718e-03
GO:BP	GO:0006638	neutral lipid metabolic process	24	134	3.797e-03
GO:BP	GO:0002520	immune system development	32	203	3.838e-03
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	20	102	3.870e-03
GO:BP	GO:0048608	reproductive structure development	44	314	3.870e-03
GO:BP	GO:0015914	phospholipid transport	20	102	3.870e-03
GO:BP	GO:0044283	small molecule biosynthetic process	72	593	3.943e-03
GO:BP	GO:0046460	neutral lipid biosynthetic process	13	51	3.983e-03
GO:BP	GO:0048514	blood vessel morphogenesis	76	635	3.983e-03
GO:BP	GO:0002428	antigen processing and presentation of peptide antigen via MHC class Ib	7	16	3.983e-03
GO:BP	GO:0021915	neural tube development	27	160	3.983e-03
GO:BP	GO:0046463	acylglycerol biosynthetic process	13	51	3.983e-03
GO:BP	GO:0048871	multicellular organismal-level homeostasis	94	825	4.043e-03
GO:BP	GO:0051223	regulation of protein transport	57	442	4.062e-03
GO:BP	GO:0060284	regulation of cell development	96	847	4.119e-03
GO:BP	GO:0006839	mitochondrial transport	29	178	4.175e-03
GO:BP	GO:0016032	viral process	55	423	4.232e-03
GO:BP	GO:0071363	cellular response to growth factor stimulus	81	689	4.244e-03
GO:BP	GO:0071559	response to transforming growth factor beta	39	269	4.296e-03
GO:BP	GO:0010647	positive regulation of cell communication	181	1795	4.509e-03
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	90	786	4.569e-03
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	128	1199	4.569e-03
GO:BP	GO:1904026	regulation of collagen fibril organization	5	8	4.697e-03
GO:BP	GO:2000973	regulation of pro-B cell differentiation	5	8	4.697e-03
GO:BP	GO:0061458	reproductive system development	44	318	4.770e-03
GO:BP	GO:0002328	pro-B cell differentiation	6	12	4.819e-03
GO:BP	GO:0019827	stem cell population maintenance	29	180	4.869e-03
GO:BP	GO:0045184	establishment of protein localization	193	1937	4.927e-03
GO:BP	GO:0009952	anterior/posterior pattern specification	34	225	4.927e-03
GO:BP	GO:0048513	animal organ development	291	3085	4.974e-03
GO:BP	GO:1904951	positive regulation of establishment of protein localization	45	329	5.116e-03
GO:BP	GO:0042982	amyloid precursor protein metabolic process	16	74	5.116e-03
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	28	172	5.129e-03
GO:BP	GO:0046486	glycerolipid metabolic process	52	398	5.239e-03
GO:BP	GO:0031400	negative regulation of protein modification process	47	349	5.239e-03
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	24	138	5.239e-03
GO:BP	GO:0051130	positive regulation of cellular component organization	119	1105	5.239e-03
GO:BP	GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	8	22	5.314e-03
GO:BP	GO:1903829	positive regulation of protein localization	62	499	5.398e-03
GO:BP	GO:0016054	organic acid catabolic process	36	246	5.816e-03
GO:BP	GO:0046395	carboxylic acid catabolic process	36	246	5.816e-03
GO:BP	GO:0006979	response to oxidative stress	52	400	5.816e-03
GO:BP	GO:0048872	homeostasis of number of cells	45	332	5.987e-03
GO:BP	GO:0044282	small molecule catabolic process	49	371	5.987e-03
GO:BP	GO:0045667	regulation of osteoblast differentiation	23	131	5.987e-03
GO:BP	GO:0048699	generation of neurons	157	1536	6.194e-03
GO:BP	GO:0070848	response to growth factor	83	721	6.261e-03
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	42	304	6.261e-03
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	42	304	6.261e-03
GO:BP	GO:0032787	monocarboxylic acid metabolic process	73	616	6.261e-03
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	132	1256	6.283e-03
GO:BP	GO:0045321	leukocyte activation	107	980	6.283e-03
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	20	107	6.283e-03
GO:BP	GO:0030098	lymphocyte differentiation	56	442	6.283e-03
GO:BP	GO:0048255	mRNA stabilization	15	69	6.752e-03
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	93	831	6.752e-03
GO:BP	GO:0060411	cardiac septum morphogenesis	15	69	6.752e-03
GO:BP	GO:0030182	neuron differentiation	149	1451	6.752e-03
GO:BP	GO:0045596	negative regulation of cell differentiation	78	671	6.752e-03
GO:BP	GO:0030199	collagen fibril organization	15	69	6.752e-03
GO:BP	GO:0043068	positive regulation of programmed cell death	66	546	6.752e-03
GO:BP	GO:0002475	antigen processing and presentation via MHC class Ib	8	23	6.752e-03
GO:BP	GO:0051348	negative regulation of transferase activity	27	167	6.752e-03
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	65	535	6.752e-03
GO:BP	GO:0006658	phosphatidylserine metabolic process	8	23	6.752e-03
GO:BP	GO:0048736	appendage development	30	194	6.752e-03
GO:BP	GO:0042632	cholesterol homeostasis	18	92	6.752e-03
GO:BP	GO:0060173	limb development	30	194	6.752e-03
GO:BP	GO:0003006	developmental process involved in reproduction	112	1038	6.752e-03
GO:BP	GO:0001525	angiogenesis	66	547	6.994e-03
GO:BP	GO:0009967	positive regulation of signal transduction	160	1578	7.173e-03
GO:BP	GO:0045017	glycerolipid biosynthetic process	36	250	7.173e-03
GO:BP	GO:0009987	cellular process	1596	20247	7.498e-03
GO:BP	GO:0043065	positive regulation of apoptotic process	64	528	7.508e-03
GO:BP	GO:0055092	sterol homeostasis	18	93	7.596e-03
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	75	643	7.607e-03
GO:BP	GO:0046165	alcohol biosynthetic process	24	143	7.864e-03
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	11	42	7.926e-03
GO:BP	GO:0008610	lipid biosynthetic process	83	729	7.926e-03
GO:BP	GO:0031946	regulation of glucocorticoid biosynthetic process	5	9	7.926e-03
GO:BP	GO:0000209	protein polyubiquitination	39	280	7.926e-03
GO:BP	GO:0048318	axial mesoderm development	5	9	7.926e-03
GO:BP	GO:0001501	skeletal system development	65	540	7.939e-03
GO:BP	GO:0050810	regulation of steroid biosynthetic process	16	78	8.008e-03
GO:BP	GO:0042987	amyloid precursor protein catabolic process	13	56	8.225e-03
GO:BP	GO:0060541	respiratory system development	33	225	8.680e-03
GO:BP	GO:0002483	antigen processing and presentation of endogenous peptide antigen	8	24	8.871e-03
GO:BP	GO:0032869	cellular response to insulin stimulus	31	207	8.944e-03
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	16	79	9.172e-03
GO:BP	GO:0048863	stem cell differentiation	35	245	9.456e-03
GO:BP	GO:0009895	negative regulation of catabolic process	47	361	9.456e-03
GO:BP	GO:0001933	negative regulation of protein phosphorylation	35	245	9.456e-03
GO:BP	GO:0030509	BMP signaling pathway	25	154	9.500e-03
GO:BP	GO:1903131	mononuclear cell differentiation	64	534	9.560e-03
GO:BP	GO:0015748	organophosphate ester transport	27	172	9.734e-03
GO:BP	GO:0002486	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	6	14	1.054e-02
GO:BP	GO:0001843	neural tube closure	17	88	1.060e-02
GO:BP	GO:0048878	chemical homeostasis	111	1043	1.081e-02
GO:BP	GO:0043067	regulation of programmed cell death	152	1506	1.150e-02
GO:BP	GO:0002181	cytoplasmic translation	26	165	1.150e-02
GO:BP	GO:0019883	antigen processing and presentation of endogenous antigen	9	31	1.154e-02
GO:BP	GO:0033077	T cell differentiation in thymus	17	89	1.194e-02
GO:BP	GO:0060606	tube closure	17	89	1.194e-02
GO:BP	GO:1901698	response to nitrogen compound	114	1080	1.208e-02
GO:BP	GO:0005975	carbohydrate metabolic process	66	561	1.253e-02
GO:BP	GO:0035621	ER to Golgi ceramide transport	3	3	1.256e-02
GO:BP	GO:0071403	cellular response to high density lipoprotein particle stimulus	3	3	1.256e-02
GO:BP	GO:0060748	tertiary branching involved in mammary gland duct morphogenesis	3	3	1.256e-02
GO:BP	GO:0002085	inhibition of neuroepithelial cell differentiation	4	6	1.280e-02
GO:BP	GO:0044093	positive regulation of molecular function	96	884	1.300e-02
GO:BP	GO:0002521	leukocyte differentiation	73	636	1.300e-02
GO:BP	GO:0030278	regulation of ossification	21	123	1.306e-02
GO:BP	GO:0042326	negative regulation of phosphorylation	36	260	1.333e-02
GO:BP	GO:0072521	purine-containing compound metabolic process	66	563	1.333e-02
GO:BP	GO:1990144	intrinsic apoptotic signaling pathway in response to hypoxia	5	10	1.333e-02
GO:BP	GO:0055088	lipid homeostasis	26	167	1.333e-02
GO:BP	GO:0000902	cell morphogenesis	106	996	1.368e-02
GO:BP	GO:0006974	DNA damage response	98	908	1.371e-02
GO:BP	GO:0019941	modification-dependent protein catabolic process	73	638	1.388e-02
GO:BP	GO:0009306	protein secretion	48	379	1.402e-02
GO:BP	GO:0060674	placenta blood vessel development	9	32	1.406e-02
GO:BP	GO:0009798	axis specification	18	99	1.437e-02
GO:BP	GO:0051259	protein complex oligomerization	37	271	1.437e-02
GO:BP	GO:0030030	cell projection organization	162	1631	1.437e-02
GO:BP	GO:0030258	lipid modification	29	196	1.487e-02
GO:BP	GO:0008283	cell population proliferation	195	2015	1.487e-02
GO:BP	GO:0090030	regulation of steroid hormone biosynthetic process	6	15	1.487e-02
GO:BP	GO:0070243	regulation of thymocyte apoptotic process	6	15	1.487e-02
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	75	662	1.515e-02
GO:BP	GO:0051168	nuclear export	26	169	1.524e-02
GO:BP	GO:0009896	positive regulation of catabolic process	64	546	1.542e-02
GO:BP	GO:0008593	regulation of Notch signaling pathway	18	100	1.587e-02
GO:BP	GO:0006644	phospholipid metabolic process	49	392	1.597e-02
GO:BP	GO:0035592	establishment of protein localization to extracellular region	48	382	1.603e-02
GO:BP	GO:0006066	alcohol metabolic process	46	362	1.611e-02
GO:BP	GO:0001701	in utero embryonic development	51	413	1.645e-02
GO:BP	GO:1902653	secondary alcohol biosynthetic process	13	61	1.684e-02
GO:BP	GO:0006695	cholesterol biosynthetic process	13	61	1.684e-02
GO:BP	GO:0001841	neural tube formation	18	101	1.758e-02
GO:BP	GO:0051604	protein maturation	63	539	1.775e-02
GO:BP	GO:0046488	phosphatidylinositol metabolic process	25	162	1.778e-02
GO:BP	GO:0010719	negative regulation of epithelial to mesenchymal transition	10	40	1.836e-02
GO:BP	GO:0006753	nucleoside phosphate metabolic process	73	646	1.837e-02
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	41	315	1.862e-02
GO:BP	GO:0003007	heart morphogenesis	36	266	1.862e-02
GO:BP	GO:0006401	RNA catabolic process	41	315	1.862e-02
GO:BP	GO:0061157	mRNA destabilization	18	102	1.933e-02
GO:BP	GO:0048534	hematopoietic or lymphoid organ development	18	102	1.933e-02
GO:BP	GO:0007507	heart development	69	605	1.941e-02
GO:BP	GO:0032940	secretion by cell	92	854	1.941e-02
GO:BP	GO:0014020	primary neural tube formation	17	94	1.989e-02
GO:BP	GO:0042981	regulation of apoptotic process	146	1462	1.990e-02
GO:BP	GO:0032870	cellular response to hormone stimulus	72	638	2.005e-02
GO:BP	GO:0097190	apoptotic signaling pathway	69	606	2.005e-02
GO:BP	GO:0043489	RNA stabilization	15	78	2.023e-02
GO:BP	GO:0032926	negative regulation of activin receptor signaling pathway	6	16	2.025e-02
GO:BP	GO:1900038	negative regulation of cellular response to hypoxia	5	11	2.025e-02
GO:BP	GO:0120009	intermembrane lipid transfer	9	34	2.025e-02
GO:BP	GO:0031943	regulation of glucocorticoid metabolic process	5	11	2.025e-02
GO:BP	GO:0038066	p38MAPK cascade	12	55	2.025e-02
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	71	628	2.025e-02
GO:BP	GO:0062197	cellular response to chemical stress	41	317	2.025e-02
GO:BP	GO:0060603	mammary gland duct morphogenesis	9	34	2.025e-02
GO:BP	GO:0007033	vacuole organization	33	239	2.033e-02
GO:BP	GO:0071692	protein localization to extracellular region	48	388	2.066e-02
GO:BP	GO:0006458	‘de novo’ protein folding	11	48	2.094e-02
GO:BP	GO:0045746	negative regulation of Notch signaling pathway	10	41	2.112e-02
GO:BP	GO:0071773	cellular response to BMP stimulus	25	165	2.154e-02
GO:BP	GO:0071772	response to BMP	25	165	2.154e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	22	138	2.154e-02
GO:BP	GO:0035116	embryonic hindlimb morphogenesis	8	28	2.210e-02
GO:BP	GO:0006650	glycerophospholipid metabolic process	40	309	2.218e-02
GO:BP	GO:0018193	peptidyl-amino acid modification	76	686	2.333e-02
GO:BP	GO:2000064	regulation of cortisol biosynthetic process	4	7	2.333e-02
GO:BP	GO:0048754	branching morphogenesis of an epithelial tube	24	157	2.344e-02
GO:BP	GO:0090183	regulation of kidney development	9	35	2.449e-02
GO:BP	GO:0045879	negative regulation of smoothened signaling pathway	9	35	2.449e-02
GO:BP	GO:0019432	triglyceride biosynthetic process	10	42	2.508e-02
GO:BP	GO:0051241	negative regulation of multicellular organismal process	112	1087	2.579e-02
GO:BP	GO:0050821	protein stabilization	31	224	2.642e-02
GO:BP	GO:0051055	negative regulation of lipid biosynthetic process	12	57	2.668e-02
GO:BP	GO:0032024	positive regulation of insulin secretion	16	89	2.734e-02
GO:BP	GO:0007389	pattern specification process	56	477	2.734e-02
GO:BP	GO:0043086	negative regulation of catalytic activity	38	293	2.734e-02
GO:BP	GO:0034375	high-density lipoprotein particle remodeling	6	17	2.734e-02
GO:BP	GO:0070935	3’-UTR-mediated mRNA stabilization	8	29	2.734e-02
GO:BP	GO:0090205	positive regulation of cholesterol metabolic process	6	17	2.734e-02
GO:BP	GO:0050779	RNA destabilization	18	106	2.757e-02
GO:BP	GO:0060395	SMAD protein signal transduction	15	81	2.771e-02
GO:BP	GO:0006575	modified amino acid metabolic process	26	178	2.833e-02
GO:BP	GO:0007548	sex differentiation	38	294	2.865e-02
GO:BP	GO:1900151	regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	7	23	2.875e-02
GO:BP	GO:0060392	negative regulation of SMAD protein signal transduction	7	23	2.875e-02
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	17	98	2.875e-02
GO:BP	GO:0035137	hindlimb morphogenesis	9	36	2.889e-02
GO:BP	GO:0050657	nucleic acid transport	24	160	2.889e-02
GO:BP	GO:0050658	RNA transport	24	160	2.889e-02
GO:BP	GO:0003206	cardiac chamber morphogenesis	20	124	2.889e-02
GO:BP	GO:0048505	regulation of timing of cell differentiation	5	12	2.911e-02
GO:BP	GO:0019318	hexose metabolic process	31	226	2.911e-02
GO:BP	GO:0022414	reproductive process	157	1608	2.944e-02
GO:BP	GO:0010498	proteasomal protein catabolic process	62	543	2.951e-02
GO:BP	GO:0009062	fatty acid catabolic process	18	107	2.967e-02
GO:BP	GO:0046434	organophosphate catabolic process	33	246	3.007e-02
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	74	673	3.057e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	77	706	3.094e-02
GO:BP	GO:0006259	DNA metabolic process	104	1005	3.094e-02
GO:BP	GO:0061138	morphogenesis of a branching epithelium	27	189	3.094e-02
GO:BP	GO:0043648	dicarboxylic acid metabolic process	17	99	3.110e-02
GO:BP	GO:1902930	regulation of alcohol biosynthetic process	11	51	3.188e-02
GO:BP	GO:0003279	cardiac septum development	18	108	3.245e-02
GO:BP	GO:1902369	negative regulation of RNA catabolic process	16	91	3.251e-02
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	8	30	3.260e-02
GO:BP	GO:0006508	proteolysis	146	1486	3.268e-02
GO:BP	GO:0043242	negative regulation of protein-containing complex disassembly	15	83	3.359e-02
GO:BP	GO:0042594	response to starvation	30	219	3.366e-02
GO:BP	GO:0006457	protein folding	30	219	3.366e-02
GO:BP	GO:0002262	myeloid cell homeostasis	26	181	3.366e-02
GO:BP	GO:0051222	positive regulation of protein transport	34	258	3.366e-02
GO:BP	GO:0003382	epithelial cell morphogenesis	9	37	3.366e-02
GO:BP	GO:0002067	glandular epithelial cell differentiation	9	37	3.366e-02
GO:BP	GO:0006403	RNA localization	28	200	3.369e-02
GO:BP	GO:0006790	sulfur compound metabolic process	39	308	3.384e-02
GO:BP	GO:0006631	fatty acid metabolic process	48	400	3.396e-02
GO:BP	GO:1904028	positive regulation of collagen fibril organization	3	4	3.427e-02
GO:BP	GO:0045632	negative regulation of mechanoreceptor differentiation	3	4	3.427e-02
GO:BP	GO:0045608	negative regulation of inner ear auditory receptor cell differentiation	3	4	3.427e-02
GO:BP	GO:2000981	negative regulation of inner ear receptor cell differentiation	3	4	3.427e-02
GO:BP	GO:0003383	apical constriction	3	4	3.427e-02
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	46	380	3.432e-02
GO:BP	GO:0006417	regulation of translation	46	380	3.432e-02
GO:BP	GO:0019080	viral gene expression	18	109	3.432e-02
GO:BP	GO:0051236	establishment of RNA localization	24	163	3.432e-02
GO:BP	GO:0043691	reverse cholesterol transport	6	18	3.432e-02
GO:BP	GO:0007042	lysosomal lumen acidification	7	24	3.432e-02
GO:BP	GO:0045995	regulation of embryonic development	16	92	3.461e-02
GO:BP	GO:0061024	membrane organization	87	821	3.467e-02
GO:BP	GO:0050708	regulation of protein secretion	35	269	3.467e-02
GO:BP	GO:0033673	negative regulation of kinase activity	22	145	3.506e-02
GO:BP	GO:0031175	neuron projection development	105	1023	3.554e-02
GO:BP	GO:0005996	monosaccharide metabolic process	33	250	3.610e-02
GO:BP	GO:0062012	regulation of small molecule metabolic process	40	320	3.625e-02
GO:BP	GO:0032868	response to insulin	35	270	3.650e-02
GO:BP	GO:0006635	fatty acid beta-oxidation	14	76	3.662e-02
GO:BP	GO:0048332	mesoderm morphogenesis	14	76	3.662e-02
GO:BP	GO:0032347	regulation of aldosterone biosynthetic process	4	8	3.674e-02
GO:BP	GO:0032344	regulation of aldosterone metabolic process	4	8	3.674e-02
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	66	594	3.755e-02
GO:BP	GO:0043534	blood vessel endothelial cell migration	19	119	3.755e-02
GO:BP	GO:0019082	viral protein processing	8	31	3.769e-02
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	9	38	3.843e-02
GO:BP	GO:0038203	TORC2 signaling	5	13	3.901e-02
GO:BP	GO:0040034	regulation of development, heterochronic	5	13	3.901e-02
GO:BP	GO:0010944	negative regulation of transcription by competitive promoter binding	5	13	3.901e-02
GO:BP	GO:1903706	regulation of hemopoiesis	50	425	3.901e-02
GO:BP	GO:0090158	endoplasmic reticulum membrane organization	5	13	3.901e-02
GO:BP	GO:0033365	protein localization to organelle	121	1209	3.913e-02
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	40	322	3.924e-02
GO:BP	GO:0051098	regulation of binding	29	213	3.981e-02
GO:BP	GO:0031109	microtubule polymerization or depolymerization	21	138	4.030e-02
GO:BP	GO:0141188	nucleic acid catabolic process	42	343	4.030e-02
GO:BP	GO:0007498	mesoderm development	21	138	4.030e-02
GO:BP	GO:0045834	positive regulation of lipid metabolic process	20	129	4.040e-02
GO:BP	GO:0016126	sterol biosynthetic process	13	69	4.078e-02
GO:BP	GO:0048666	neuron development	118	1177	4.084e-02
GO:BP	GO:0050790	regulation of catalytic activity	96	928	4.084e-02
GO:BP	GO:0140352	export from cell	96	928	4.084e-02
GO:BP	GO:0045137	development of primary sexual characteristics	32	243	4.104e-02
GO:BP	GO:0032925	regulation of activin receptor signaling pathway	7	25	4.126e-02
GO:BP	GO:0097150	neuronal stem cell population maintenance	7	25	4.126e-02
GO:BP	GO:0038202	TORC1 signaling	17	103	4.205e-02
GO:BP	GO:0009725	response to hormone	94	907	4.227e-02
GO:BP	GO:1903830	magnesium ion transmembrane transport	6	19	4.297e-02
GO:BP	GO:0006491	N-glycan processing	6	19	4.297e-02
GO:BP	GO:0043433	negative regulation of DNA-binding transcription factor activity	20	130	4.316e-02
GO:BP	GO:0051028	mRNA transport	20	130	4.316e-02
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	66	599	4.336e-02
GO:BP	GO:0031647	regulation of protein stability	41	335	4.382e-02
GO:BP	GO:0008202	steroid metabolic process	41	335	4.382e-02
GO:BP	GO:0060323	head morphogenesis	9	39	4.382e-02
GO:BP	GO:0035751	regulation of lysosomal lumen pH	8	32	4.393e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	38	305	4.487e-02
GO:BP	GO:0009267	cellular response to starvation	25	177	4.487e-02
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	13	70	4.487e-02
GO:BP	GO:0044272	sulfur compound biosynthetic process	22	149	4.509e-02
GO:BP	GO:0001763	morphogenesis of a branching structure	28	206	4.549e-02
GO:BP	GO:0035050	embryonic heart tube development	15	87	4.643e-02
GO:BP	GO:0050673	epithelial cell proliferation	51	441	4.744e-02
GO:BP	GO:0042113	B cell activation	36	286	4.771e-02
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	10	47	4.804e-02
GO:BP	GO:1903432	regulation of TORC1 signaling	16	96	4.830e-02
GO:BP	GO:0050714	positive regulation of protein secretion	22	150	4.838e-02
KEGG	KEGG:04218	Cellular senescence	30	155	6.753e-03
KEGG	KEGG:01522	Endocrine resistance	22	95	6.753e-03
KEGG	KEGG:00513	Various types of N-glycan biosynthesis	13	42	6.753e-03
KEGG	KEGG:00310	Lysine degradation	16	63	1.069e-02
KEGG	KEGG:04912	GnRH signaling pathway	20	93	1.299e-02
KEGG	KEGG:05223	Non-small cell lung cancer	17	72	1.299e-02
KEGG	KEGG:00071	Fatty acid degradation	12	43	1.441e-02
KEGG	KEGG:05224	Breast cancer	27	147	1.441e-02
KEGG	KEGG:04919	Thyroid hormone signaling pathway	23	121	1.845e-02
KEGG	KEGG:05163	Human cytomegalovirus infection	36	223	1.845e-02
KEGG	KEGG:04934	Cushing syndrome	27	153	1.973e-02
KEGG	KEGG:04915	Estrogen signaling pathway	24	136	2.661e-02
KEGG	KEGG:04070	Phosphatidylinositol signaling system	19	97	2.661e-02
KEGG	KEGG:04550	Signaling pathways regulating pluripotency of stem cells	25	143	2.661e-02
KEGG	KEGG:05225	Hepatocellular carcinoma	28	166	2.661e-02
KEGG	KEGG:04750	Inflammatory mediator regulation of TRP channels	19	98	2.661e-02
KEGG	KEGG:04929	GnRH secretion	14	64	3.239e-02
KEGG	KEGG:05226	Gastric cancer	25	148	3.564e-02
KEGG	KEGG:05200	Pathways in cancer	68	527	3.697e-02
KEGG	KEGG:04540	Gap junction	17	88	3.913e-02
KEGG	KEGG:00510	N-Glycan biosynthesis	12	53	4.066e-02
KEGG	KEGG:04935	Growth hormone synthesis, secretion and action	21	120	4.204e-02
KEGG	KEGG:05214	Glioma	15	75	4.244e-02
KEGG	KEGG:00280	Valine, leucine and isoleucine degradation	11	48	4.687e-02
KEGG	KEGG:04350	TGF-beta signaling pathway	19	107	4.687e-02
KEGG	KEGG:03083	Polycomb repressive complex	16	84	4.687e-02

#write.csv(table_DOX24_up_genes, "output/table_DOX24_upreg_genes.csv")

#GO:BP
table_DOX24_up_genes_GOBP <- table_DOX24_up_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(table_motif1_GOBP_d, "data/table_motif1_GOBP_d.RDS")

table_DOX24_up_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific Up DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-2.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24_up_genes_KEGG <- table_DOX24_up_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24_up_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific Up DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-3.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX24 Downregulated Genes#####
D24_DEGs_down_mat <- as.matrix(DOX24T_DEGs_GO_down)

DOX_24_down_dxr_gene <- gost(query = D24_DEGs_down_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24_down_gost_genes <- gostplot(DOX_24_down_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24_down_gost_genes

table_DOX24_down_genes <- DOX_24_down_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24_down_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	779	5390	2.491e-36
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	608	3990	1.326e-32
GO:BP	GO:0006351	DNA-templated transcription	554	3549	6.014e-32
GO:BP	GO:0051252	regulation of RNA metabolic process	560	3687	4.144e-29
GO:BP	GO:2001141	regulation of RNA biosynthetic process	523	3428	3.183e-27
GO:BP	GO:0006355	regulation of DNA-templated transcription	520	3409	4.438e-27
GO:BP	GO:0006996	organelle organization	533	3594	7.833e-25
GO:BP	GO:0140053	mitochondrial gene expression	68	168	2.418e-23
GO:BP	GO:0044238	primary metabolic process	1413	12342	3.051e-23
GO:BP	GO:0019538	protein metabolic process	647	4721	5.580e-22
GO:BP	GO:0006366	transcription by RNA polymerase II	417	2711	1.821e-21
GO:BP	GO:0060255	regulation of macromolecule metabolic process	823	6492	2.193e-19
GO:BP	GO:0019222	regulation of metabolic process	877	7035	5.043e-19
GO:BP	GO:0006412	translation	155	727	5.342e-19
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	390	2578	1.463e-18
GO:BP	GO:0043412	macromolecule modification	442	3030	1.955e-18
GO:BP	GO:0032543	mitochondrial translation	53	130	2.466e-18
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	459	3288	1.407e-15
GO:BP	GO:0006399	tRNA metabolic process	65	210	2.240e-15
GO:BP	GO:0008152	metabolic process	1534	14136	6.307e-15
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	311	2036	7.340e-15
GO:BP	GO:0042254	ribosome biogenesis	83	323	1.691e-14
GO:BP	GO:0006139	nucleobase-containing compound metabolic process	946	7992	4.027e-14
GO:BP	GO:0043170	macromolecule metabolic process	1336	12048	9.159e-14
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	703	5644	1.266e-13
GO:BP	GO:0046907	intracellular transport	226	1381	1.531e-13
GO:BP	GO:0051254	positive regulation of RNA metabolic process	281	1835	1.986e-13
GO:BP	GO:0010468	regulation of gene expression	690	5536	2.275e-13
GO:BP	GO:0009893	positive regulation of metabolic process	481	3597	3.676e-13
GO:BP	GO:0016072	rRNA metabolic process	70	266	9.680e-13
GO:BP	GO:0009889	regulation of biosynthetic process	714	5809	1.238e-12
GO:BP	GO:0009057	macromolecule catabolic process	225	1417	4.106e-12
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	259	1697	4.106e-12
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	259	1699	4.513e-12
GO:BP	GO:0090304	nucleic acid metabolic process	876	7434	5.303e-12
GO:BP	GO:0051649	establishment of localization in cell	295	2010	6.845e-12
GO:BP	GO:0036211	protein modification process	389	2846	1.566e-11
GO:BP	GO:0009056	catabolic process	363	2639	5.516e-11
GO:BP	GO:0006259	DNA metabolic process	169	1005	6.692e-11
GO:BP	GO:0033043	regulation of organelle organization	187	1148	6.702e-11
GO:BP	GO:0008033	tRNA processing	43	139	4.309e-10
GO:BP	GO:0009451	RNA modification	49	174	6.303e-10
GO:BP	GO:0015031	protein transport	219	1444	8.098e-10
GO:BP	GO:0048522	positive regulation of cellular process	706	5920	1.175e-09
GO:BP	GO:0006364	rRNA processing	57	225	1.246e-09
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	350	2593	1.657e-09
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	136	786	1.657e-09
GO:BP	GO:0033554	cellular response to stress	263	1830	1.680e-09
GO:BP	GO:0006281	DNA repair	114	621	1.864e-09
GO:BP	GO:0034654	nucleobase-containing compound biosynthetic process	822	7076	1.864e-09
GO:BP	GO:0033036	macromolecule localization	419	3228	2.494e-09
GO:BP	GO:0051641	cellular localization	465	3661	3.594e-09
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	116	643	3.600e-09
GO:BP	GO:0006974	DNA damage response	150	908	4.395e-09
GO:BP	GO:0019941	modification-dependent protein catabolic process	115	638	4.477e-09
GO:BP	GO:0030163	protein catabolic process	165	1030	5.069e-09
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	113	628	7.193e-09
GO:BP	GO:0070727	cellular macromolecule localization	367	2782	7.625e-09
GO:BP	GO:0016070	RNA metabolic process	796	6873	9.372e-09
GO:BP	GO:0008104	protein localization	365	2770	9.621e-09
GO:BP	GO:0048518	positive regulation of biological process	734	6264	9.621e-09
GO:BP	GO:0009891	positive regulation of biosynthetic process	356	2696	1.334e-08
GO:BP	GO:0033044	regulation of chromosome organization	57	242	1.965e-08
GO:BP	GO:0006886	intracellular protein transport	119	686	2.130e-08
GO:BP	GO:0007005	mitochondrion organization	85	435	2.583e-08
GO:BP	GO:0141187	nucleic acid biosynthetic process	783	6782	2.770e-08
GO:BP	GO:0071705	nitrogen compound transport	267	1923	3.215e-08
GO:BP	GO:0043687	post-translational protein modification	161	1027	3.856e-08
GO:BP	GO:0051128	regulation of cellular component organization	324	2433	3.908e-08
GO:BP	GO:0010498	proteasomal protein catabolic process	99	543	4.473e-08
GO:BP	GO:0051052	regulation of DNA metabolic process	93	500	5.161e-08
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	81	414	5.820e-08
GO:BP	GO:0006325	chromatin organization	142	884	8.053e-08
GO:BP	GO:1903008	organelle disassembly	26	71	8.857e-08
GO:BP	GO:0009894	regulation of catabolic process	161	1040	8.954e-08
GO:BP	GO:0016073	snRNA metabolic process	23	58	1.303e-07
GO:BP	GO:0032774	RNA biosynthetic process	766	6671	1.381e-07
GO:BP	GO:0032790	ribosome disassembly	19	41	1.479e-07
GO:BP	GO:0032446	protein modification by small protein conjugation	137	853	1.515e-07
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	152	975	1.561e-07
GO:BP	GO:0043414	macromolecule methylation	36	127	1.930e-07
GO:BP	GO:0043484	regulation of RNA splicing	46	187	1.976e-07
GO:BP	GO:0009987	cellular process	2002	20247	2.072e-07
GO:BP	GO:0006403	RNA localization	48	200	2.089e-07
GO:BP	GO:0006400	tRNA modification	30	95	2.456e-07
GO:BP	GO:0050789	regulation of biological process	1316	12336	2.502e-07
GO:BP	GO:0009059	macromolecule biosynthetic process	1058	9643	2.537e-07
GO:BP	GO:0050794	regulation of cellular process	1278	11946	3.407e-07
GO:BP	GO:0061919	process utilizing autophagic mechanism	103	597	3.517e-07
GO:BP	GO:0006914	autophagy	103	597	3.517e-07
GO:BP	GO:0071840	cellular component organization or biogenesis	933	8393	4.831e-07
GO:BP	GO:0051726	regulation of cell cycle	163	1087	5.831e-07
GO:BP	GO:0009058	biosynthetic process	1152	10664	8.796e-07
GO:BP	GO:0032259	methylation	52	236	9.568e-07
GO:BP	GO:0032204	regulation of telomere maintenance	32	112	1.016e-06
GO:BP	GO:0045184	establishment of protein localization	260	1937	1.016e-06
GO:BP	GO:0006302	double-strand break repair	64	319	1.016e-06
GO:BP	GO:0070925	organelle assembly	157	1046	1.016e-06
GO:BP	GO:0065007	biological regulation	1348	12743	1.285e-06
GO:BP	GO:0007049	cell cycle	228	1663	1.540e-06
GO:BP	GO:0072344	rescue of stalled ribosome	16	34	1.728e-06
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	34	127	2.074e-06
GO:BP	GO:0051276	chromosome organization	97	574	2.512e-06
GO:BP	GO:0051246	regulation of protein metabolic process	248	1855	3.098e-06
GO:BP	GO:0010467	gene expression	1007	9224	3.214e-06
GO:BP	GO:0006282	regulation of DNA repair	49	225	3.285e-06
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	91	535	4.717e-06
GO:BP	GO:0006354	DNA-templated transcription elongation	34	134	8.176e-06
GO:BP	GO:0009896	positive regulation of catabolic process	91	546	1.203e-05
GO:BP	GO:1903311	regulation of mRNA metabolic process	60	312	1.214e-05
GO:BP	GO:0006338	chromatin remodeling	113	725	1.507e-05
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	176	1256	1.543e-05
GO:BP	GO:0031123	RNA 3’-end processing	27	96	1.662e-05
GO:BP	GO:0016567	protein ubiquitination	118	768	1.706e-05
GO:BP	GO:0000723	telomere maintenance	38	164	1.827e-05
GO:BP	GO:0038202	TORC1 signaling	28	103	2.122e-05
GO:BP	GO:0006402	mRNA catabolic process	52	261	2.386e-05
GO:BP	GO:0001510	RNA methylation	24	81	2.551e-05
GO:BP	GO:0000725	recombinational repair	42	193	2.672e-05
GO:BP	GO:0000724	double-strand break repair via homologous recombination	41	188	3.412e-05
GO:BP	GO:0051168	nuclear export	38	169	3.897e-05
GO:BP	GO:0006289	nucleotide-excision repair	24	83	4.055e-05
GO:BP	GO:1903047	mitotic cell cycle process	113	745	5.453e-05
GO:BP	GO:0080135	regulation of cellular response to stress	85	519	5.670e-05
GO:BP	GO:0051054	positive regulation of DNA metabolic process	55	291	6.076e-05
GO:BP	GO:0000966	RNA 5’-end processing	15	38	6.378e-05
GO:BP	GO:0000278	mitotic cell cycle	130	892	7.232e-05
GO:BP	GO:0031929	TOR signaling	37	167	7.533e-05
GO:BP	GO:0022411	cellular component disassembly	75	446	8.634e-05
GO:BP	GO:2000779	regulation of double-strand break repair	33	143	1.060e-04
GO:BP	GO:0051236	establishment of RNA localization	36	163	1.102e-04
GO:BP	GO:0016180	snRNA processing	14	35	1.147e-04
GO:BP	GO:0006417	regulation of translation	66	380	1.147e-04
GO:BP	GO:0009303	rRNA transcription	15	40	1.293e-04
GO:BP	GO:0007007	inner mitochondrial membrane organization	16	45	1.349e-04
GO:BP	GO:0006401	RNA catabolic process	57	315	1.502e-04
GO:BP	GO:0032006	regulation of TOR signaling	33	146	1.635e-04
GO:BP	GO:0000209	protein polyubiquitination	52	280	1.839e-04
GO:BP	GO:0050684	regulation of mRNA processing	31	134	1.906e-04
GO:BP	GO:0006383	transcription by RNA polymerase III	19	62	1.971e-04
GO:BP	GO:0006913	nucleocytoplasmic transport	59	334	2.134e-04
GO:BP	GO:0051169	nuclear transport	59	334	2.134e-04
GO:BP	GO:0032007	negative regulation of TOR signaling	20	68	2.186e-04
GO:BP	GO:0048193	Golgi vesicle transport	56	312	2.235e-04
GO:BP	GO:0022402	cell cycle process	172	1280	2.291e-04
GO:BP	GO:0000959	mitochondrial RNA metabolic process	17	52	2.291e-04
GO:BP	GO:0016197	endosomal transport	53	290	2.291e-04
GO:BP	GO:0006414	translational elongation	22	80	2.421e-04
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	29	123	2.439e-04
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	36	170	2.685e-04
GO:BP	GO:0045739	positive regulation of DNA repair	31	137	2.859e-04
GO:BP	GO:1904262	negative regulation of TORC1 signaling	16	48	3.154e-04
GO:BP	GO:0010564	regulation of cell cycle process	106	720	3.729e-04
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	13	34	4.167e-04
GO:BP	GO:0050657	nucleic acid transport	34	160	4.283e-04
GO:BP	GO:0050658	RNA transport	34	160	4.283e-04
GO:BP	GO:0010638	positive regulation of organelle organization	78	492	4.283e-04
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	22	83	4.321e-04
GO:BP	GO:0007004	telomere maintenance via telomerase	18	60	4.321e-04
GO:BP	GO:0018205	peptidyl-lysine modification	31	140	4.321e-04
GO:BP	GO:0141188	nucleic acid catabolic process	59	343	4.394e-04
GO:BP	GO:0006352	DNA-templated transcription initiation	41	210	4.795e-04
GO:BP	GO:1903432	regulation of TORC1 signaling	24	96	5.006e-04
GO:BP	GO:0000154	rRNA modification	13	35	5.675e-04
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	20	73	6.181e-04
GO:BP	GO:0032200	telomere organization	38	191	6.225e-04
GO:BP	GO:0016043	cellular component organization	880	8184	6.783e-04
GO:BP	GO:0006390	mitochondrial transcription	10	22	7.049e-04
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	44	236	7.446e-04
GO:BP	GO:0002183	cytoplasmic translational initiation	15	46	7.446e-04
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	27	118	8.004e-04
GO:BP	GO:0015931	nucleobase-containing compound transport	44	237	8.205e-04
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	18	63	8.434e-04
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	196	1529	8.494e-04
GO:BP	GO:0051247	positive regulation of protein metabolic process	141	1039	8.774e-04
GO:BP	GO:0070585	protein localization to mitochondrion	29	132	8.774e-04
GO:BP	GO:0018193	peptidyl-amino acid modification	100	686	8.774e-04
GO:BP	GO:0032206	positive regulation of telomere maintenance	20	75	8.864e-04
GO:BP	GO:0042176	regulation of protein catabolic process	61	369	9.852e-04
GO:BP	GO:0030522	intracellular receptor signaling pathway	62	377	9.906e-04
GO:BP	GO:0017004	cytochrome complex assembly	14	42	1.002e-03
GO:BP	GO:0016236	macroautophagy	60	362	1.040e-03
GO:BP	GO:0042273	ribosomal large subunit biogenesis	19	70	1.051e-03
GO:BP	GO:0007346	regulation of mitotic cell cycle	76	492	1.185e-03
GO:BP	GO:0061024	membrane organization	115	821	1.257e-03
GO:BP	GO:0007006	mitochondrial membrane organization	26	116	1.528e-03
GO:BP	GO:0051028	mRNA transport	28	130	1.674e-03
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	16	55	1.740e-03
GO:BP	GO:0006405	RNA export from nucleus	22	91	1.740e-03
GO:BP	GO:0009895	negative regulation of catabolic process	59	361	1.758e-03
GO:BP	GO:0006626	protein targeting to mitochondrion	24	104	1.765e-03
GO:BP	GO:0042274	ribosomal small subunit biogenesis	24	104	1.765e-03
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	13	39	1.824e-03
GO:BP	GO:0070979	protein K11-linked ubiquitination	13	39	1.824e-03
GO:BP	GO:0060341	regulation of cellular localization	136	1013	1.856e-03
GO:BP	GO:0099116	tRNA 5’-end processing	8	16	1.895e-03
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	25	112	2.172e-03
GO:BP	GO:0007030	Golgi organization	31	153	2.187e-03
GO:BP	GO:0035556	intracellular signal transduction	346	2965	2.331e-03
GO:BP	GO:0140694	membraneless organelle assembly	67	430	2.428e-03
GO:BP	GO:0000819	sister chromatid segregation	42	234	2.429e-03
GO:BP	GO:0000460	maturation of 5.8S rRNA	12	35	2.503e-03
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	54	327	2.569e-03
GO:BP	GO:0010506	regulation of autophagy	59	367	2.642e-03
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	31	155	2.731e-03
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	14	46	2.759e-03
GO:BP	GO:0001682	tRNA 5’-leader removal	7	13	2.990e-03
GO:BP	GO:0031503	protein-containing complex localization	39	215	3.334e-03
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	26	122	3.350e-03
GO:BP	GO:0043038	amino acid activation	14	47	3.514e-03
GO:BP	GO:0034198	cellular response to amino acid starvation	15	53	3.785e-03
GO:BP	GO:0030490	maturation of SSU-rRNA	15	53	3.785e-03
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	27	130	3.859e-03
GO:BP	GO:0010256	endomembrane system organization	88	613	3.863e-03
GO:BP	GO:0006360	transcription by RNA polymerase I	18	71	3.863e-03
GO:BP	GO:0044782	cilium organization	66	431	4.289e-03
GO:BP	GO:0006513	protein monoubiquitination	14	48	4.377e-03
GO:BP	GO:0051053	negative regulation of DNA metabolic process	28	139	4.928e-03
GO:BP	GO:0010639	negative regulation of organelle organization	56	352	4.928e-03
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	36	197	4.949e-03
GO:BP	GO:0006418	tRNA aminoacylation for protein translation	13	43	4.990e-03
GO:BP	GO:0043144	sno(s)RNA processing	7	14	5.110e-03
GO:BP	GO:0006370	7-methylguanosine mRNA capping	5	7	5.202e-03
GO:BP	GO:0040031	snRNA modification	5	7	5.202e-03
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	22	99	5.564e-03
GO:BP	GO:2000781	positive regulation of double-strand break repair	21	93	6.100e-03
GO:BP	GO:0007017	microtubule-based process	131	999	6.222e-03
GO:BP	GO:0071806	protein transmembrane transport	18	74	6.405e-03
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	25	121	6.898e-03
GO:BP	GO:1990928	response to amino acid starvation	15	56	6.898e-03
GO:BP	GO:0090685	RNA localization to nucleus	8	19	7.117e-03
GO:BP	GO:0090672	telomerase RNA localization	8	19	7.117e-03
GO:BP	GO:0090671	telomerase RNA localization to Cajal body	8	19	7.117e-03
GO:BP	GO:0090670	RNA localization to Cajal body	8	19	7.117e-03
GO:BP	GO:0071025	RNA surveillance	8	19	7.117e-03
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	85	600	7.156e-03
GO:BP	GO:0062125	regulation of mitochondrial gene expression	11	34	7.730e-03
GO:BP	GO:0071028	nuclear mRNA surveillance	6	11	7.914e-03
GO:BP	GO:0006488	dolichol-linked oligosaccharide biosynthetic process	9	24	7.914e-03
GO:BP	GO:0042790	nucleolar large rRNA transcription by RNA polymerase I	9	24	7.914e-03
GO:BP	GO:1902531	regulation of intracellular signal transduction	234	1953	7.914e-03
GO:BP	GO:0062028	regulation of stress granule assembly	6	11	7.914e-03
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	9	24	7.914e-03
GO:BP	GO:0034315	regulation of Arp2/3 complex-mediated actin nucleation	10	29	7.924e-03
GO:BP	GO:0043248	proteasome assembly	7	15	7.924e-03
GO:BP	GO:0071027	nuclear RNA surveillance	7	15	7.924e-03
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	28	144	8.123e-03
GO:BP	GO:0016192	vesicle-mediated transport	195	1592	8.301e-03
GO:BP	GO:0051179	localization	604	5555	8.322e-03
GO:BP	GO:0030488	tRNA methylation	12	40	8.571e-03
GO:BP	GO:0006457	protein folding	38	219	8.647e-03
GO:BP	GO:0007010	cytoskeleton organization	188	1529	8.670e-03
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	32	174	8.723e-03
GO:BP	GO:0006406	mRNA export from nucleus	17	70	8.764e-03
GO:BP	GO:0140014	mitotic nuclear division	46	282	9.062e-03
GO:BP	GO:0141084	inflammasome-mediated signaling pathway	13	46	9.062e-03
GO:BP	GO:0043039	tRNA aminoacylation	13	46	9.062e-03
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	11	35	9.457e-03
GO:BP	GO:0006310	DNA recombination	54	347	9.531e-03
GO:BP	GO:0007264	small GTPase-mediated signal transduction	73	505	9.706e-03
GO:BP	GO:2001251	negative regulation of chromosome organization	21	97	9.752e-03
GO:BP	GO:0030150	protein import into mitochondrial matrix	8	20	9.752e-03
GO:BP	GO:0008535	respiratory chain complex IV assembly	10	30	1.015e-02
GO:BP	GO:0141085	regulation of inflammasome-mediated signaling pathway	12	41	1.047e-02
GO:BP	GO:0000226	microtubule cytoskeleton organization	92	670	1.060e-02
GO:BP	GO:0009452	7-methylguanosine RNA capping	5	8	1.075e-02
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	13	47	1.100e-02
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	22	105	1.127e-02
GO:BP	GO:2001252	positive regulation of chromosome organization	22	105	1.127e-02
GO:BP	GO:0051493	regulation of cytoskeleton organization	74	517	1.147e-02
GO:BP	GO:0032978	protein insertion into membrane from inner side	4	5	1.152e-02
GO:BP	GO:0032979	protein insertion into mitochondrial inner membrane from matrix	4	5	1.152e-02
GO:BP	GO:0016074	sno(s)RNA metabolic process	7	16	1.159e-02
GO:BP	GO:0036260	RNA capping	7	16	1.159e-02
GO:BP	GO:1902745	positive regulation of lamellipodium organization	11	36	1.167e-02
GO:BP	GO:0010212	response to ionizing radiation	27	141	1.197e-02
GO:BP	GO:0000070	mitotic sister chromatid segregation	34	193	1.201e-02
GO:BP	GO:0030031	cell projection assembly	85	613	1.221e-02
GO:BP	GO:0006413	translational initiation	25	127	1.237e-02
GO:BP	GO:0031126	sno(s)RNA 3’-end processing	6	12	1.248e-02
GO:BP	GO:0045732	positive regulation of protein catabolic process	36	209	1.270e-02
GO:BP	GO:0034314	Arp2/3 complex-mediated actin nucleation	13	48	1.303e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	9	26	1.359e-02
GO:BP	GO:0060271	cilium assembly	60	403	1.370e-02
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	31	172	1.371e-02
GO:BP	GO:0032880	regulation of protein localization	118	907	1.380e-02
GO:BP	GO:0032984	protein-containing complex disassembly	42	257	1.385e-02
GO:BP	GO:0010948	negative regulation of cell cycle process	46	289	1.397e-02
GO:BP	GO:0006893	Golgi to plasma membrane transport	16	67	1.408e-02
GO:BP	GO:0048284	organelle fusion	30	165	1.415e-02
GO:BP	GO:1902115	regulation of organelle assembly	39	234	1.435e-02
GO:BP	GO:0033365	protein localization to organelle	151	1209	1.520e-02
GO:BP	GO:0006487	protein N-linked glycosylation	17	74	1.520e-02
GO:BP	GO:1905168	positive regulation of double-strand break repair via homologous recombination	12	43	1.520e-02
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	14	55	1.520e-02
GO:BP	GO:0006508	proteolysis	181	1486	1.520e-02
GO:BP	GO:0048523	negative regulation of cellular process	607	5629	1.591e-02
GO:BP	GO:0051640	organelle localization	85	620	1.629e-02
GO:BP	GO:0048285	organelle fission	71	500	1.682e-02
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	42	260	1.689e-02
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	9	27	1.753e-02
GO:BP	GO:0009966	regulation of signal transduction	343	3034	1.783e-02
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	26	138	1.783e-02
GO:BP	GO:0034472	snRNA 3’-end processing	8	22	1.786e-02
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	41	253	1.787e-02
GO:BP	GO:0141137	positive regulation of gene expression, epigenetic	14	56	1.787e-02
GO:BP	GO:0051253	negative regulation of RNA metabolic process	171	1400	1.825e-02
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	16	69	1.868e-02
GO:BP	GO:0016050	vesicle organization	56	376	1.884e-02
GO:BP	GO:0009304	tRNA transcription	6	13	1.922e-02
GO:BP	GO:0007059	chromosome segregation	62	427	1.957e-02
GO:BP	GO:1901987	regulation of cell cycle phase transition	62	427	1.957e-02
GO:BP	GO:0051865	protein autoubiquitination	17	76	1.975e-02
GO:BP	GO:0051983	regulation of chromosome segregation	25	132	1.993e-02
GO:BP	GO:0009218	pyrimidine ribonucleotide metabolic process	10	33	1.995e-02
GO:BP	GO:0006997	nucleus organization	27	147	2.048e-02
GO:BP	GO:0009166	nucleotide catabolic process	29	162	2.050e-02
GO:BP	GO:0030307	positive regulation of cell growth	29	162	2.050e-02
GO:BP	GO:0080134	regulation of response to stress	169	1387	2.104e-02
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	89	662	2.107e-02
GO:BP	GO:0032205	negative regulation of telomere maintenance	11	39	2.107e-02
GO:BP	GO:0044087	regulation of cellular component biogenesis	128	1011	2.107e-02
GO:BP	GO:0007031	peroxisome organization	11	39	2.107e-02
GO:BP	GO:0051125	regulation of actin nucleation	11	39	2.107e-02
GO:BP	GO:2000780	negative regulation of double-strand break repair	11	39	2.107e-02
GO:BP	GO:0140285	endosome fission	3	3	2.112e-02
GO:BP	GO:0009195	pyrimidine ribonucleoside diphosphate catabolic process	3	3	2.112e-02
GO:BP	GO:0070478	nuclear-transcribed mRNA catabolic process, 3’-5’ exonucleolytic nonsense-mediated decay	3	3	2.112e-02
GO:BP	GO:0009140	pyrimidine nucleoside diphosphate catabolic process	3	3	2.112e-02
GO:BP	GO:0016094	polyprenol biosynthetic process	3	3	2.112e-02
GO:BP	GO:0031120	snRNA pseudouridine synthesis	3	3	2.112e-02
GO:BP	GO:0006256	UDP catabolic process	3	3	2.112e-02
GO:BP	GO:0002128	tRNA nucleoside ribose methylation	3	3	2.112e-02
GO:BP	GO:2000819	regulation of nucleotide-excision repair	9	28	2.117e-02
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	9	28	2.117e-02
GO:BP	GO:0006839	mitochondrial transport	31	178	2.117e-02
GO:BP	GO:0141086	negative regulation of inflammasome-mediated signaling pathway	7	18	2.204e-02
GO:BP	GO:0051130	positive regulation of cellular component organization	138	1105	2.250e-02
GO:BP	GO:0090042	tubulin deacetylation	8	23	2.250e-02
GO:BP	GO:0009259	ribonucleotide metabolic process	55	372	2.259e-02
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	21	105	2.261e-02
GO:BP	GO:0098732	macromolecule deacylation	14	58	2.325e-02
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	16	71	2.333e-02
GO:BP	GO:0032386	regulation of intracellular transport	42	266	2.341e-02
GO:BP	GO:0098813	nuclear chromosome segregation	49	323	2.341e-02
GO:BP	GO:0051129	negative regulation of cellular component organization	93	701	2.343e-02
GO:BP	GO:0071897	DNA biosynthetic process	30	172	2.387e-02
GO:BP	GO:0035966	response to topologically incorrect protein	28	157	2.407e-02
GO:BP	GO:0030520	estrogen receptor signaling pathway	13	52	2.407e-02
GO:BP	GO:0048583	regulation of response to stimulus	439	3993	2.407e-02
GO:BP	GO:0006796	phosphate-containing compound metabolic process	276	2407	2.419e-02
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	22	113	2.437e-02
GO:BP	GO:0044546	NLRP3 inflammasome complex assembly	11	40	2.437e-02
GO:BP	GO:0031124	mRNA 3’-end processing	12	46	2.438e-02
GO:BP	GO:1990116	ribosome-associated ubiquitin-dependent protein catabolic process	4	6	2.438e-02
GO:BP	GO:0000389	mRNA 3’-splice site recognition	4	6	2.438e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	19	92	2.467e-02
GO:BP	GO:0070936	protein K48-linked ubiquitination	20	99	2.467e-02
GO:BP	GO:0006793	phosphorus metabolic process	276	2410	2.545e-02
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	41	260	2.621e-02
GO:BP	GO:0006998	nuclear envelope organization	14	59	2.635e-02
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	25	136	2.698e-02
GO:BP	GO:0009150	purine ribonucleotide metabolic process	52	351	2.732e-02
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	19	93	2.766e-02
GO:BP	GO:0010507	negative regulation of autophagy	19	93	2.766e-02
GO:BP	GO:0051604	protein maturation	74	539	2.772e-02
GO:BP	GO:0031647	regulation of protein stability	50	335	2.817e-02
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	8	24	2.847e-02
GO:BP	GO:1902116	negative regulation of organelle assembly	12	47	2.871e-02
GO:BP	GO:0044772	mitotic cell cycle phase transition	61	428	2.871e-02
GO:BP	GO:0045738	negative regulation of DNA repair	11	41	2.895e-02
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	7	19	2.897e-02
GO:BP	GO:0016559	peroxisome fission	5	10	2.897e-02
GO:BP	GO:1901838	positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	5	10	2.897e-02
GO:BP	GO:0000492	box C/D snoRNP assembly	5	10	2.897e-02
GO:BP	GO:0018216	peptidyl-arginine methylation	5	10	2.897e-02
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	16	73	2.905e-02
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	18	87	3.043e-02
GO:BP	GO:0045727	positive regulation of translation	25	138	3.187e-02
GO:BP	GO:1904263	positive regulation of TORC1 signaling	13	54	3.211e-02
GO:BP	GO:1904357	negative regulation of telomere maintenance via telomere lengthening	9	30	3.239e-02
GO:BP	GO:0019693	ribose phosphate metabolic process	55	380	3.288e-02
GO:BP	GO:0035967	cellular response to topologically incorrect protein	21	109	3.302e-02
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	29	169	3.334e-02
GO:BP	GO:0006479	protein methylation	12	48	3.334e-02
GO:BP	GO:0071763	nuclear membrane organization	12	48	3.334e-02
GO:BP	GO:0008213	protein alkylation	12	48	3.334e-02
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	11	42	3.418e-02
GO:BP	GO:0140632	canonical inflammasome complex assembly	11	42	3.418e-02
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	25	139	3.432e-02
GO:BP	GO:0010646	regulation of cell communication	385	3486	3.432e-02
GO:BP	GO:1901292	nucleoside phosphate catabolic process	31	185	3.435e-02
GO:BP	GO:0043487	regulation of RNA stability	32	193	3.479e-02
GO:BP	GO:0033123	positive regulation of purine nucleotide catabolic process	8	25	3.529e-02
GO:BP	GO:1903241	U2-type prespliceosome assembly	8	25	3.529e-02
GO:BP	GO:0030813	positive regulation of nucleotide catabolic process	8	25	3.529e-02
GO:BP	GO:0045821	positive regulation of glycolytic process	8	25	3.529e-02
GO:BP	GO:0000470	maturation of LSU-rRNA	8	25	3.529e-02
GO:BP	GO:0023051	regulation of signaling	384	3478	3.529e-02
GO:BP	GO:1990778	protein localization to cell periphery	53	365	3.529e-02
GO:BP	GO:1901836	regulation of transcription of nucleolar large rRNA by RNA polymerase I	6	15	3.603e-02
GO:BP	GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process	13	55	3.603e-02
GO:BP	GO:1900226	negative regulation of NLRP3 inflammasome complex assembly	6	15	3.603e-02
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	20	103	3.603e-02
GO:BP	GO:0150011	regulation of neuron projection arborization	6	15	3.603e-02
GO:BP	GO:0045089	positive regulation of innate immune response	54	374	3.603e-02
GO:BP	GO:0006220	pyrimidine nucleotide metabolic process	13	55	3.603e-02
GO:BP	GO:0040029	epigenetic regulation of gene expression	45	299	3.617e-02
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	16	75	3.617e-02
GO:BP	GO:0006986	response to unfolded protein	25	140	3.622e-02
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	19	96	3.628e-02
GO:BP	GO:0043543	protein acylation	18	89	3.654e-02
GO:BP	GO:0018200	peptidyl-glutamic acid modification	7	20	3.676e-02
GO:BP	GO:0009301	snRNA transcription	7	20	3.676e-02
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	22	118	3.712e-02
GO:BP	GO:0042073	intraciliary transport	12	49	3.752e-02
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	24	133	3.754e-02
GO:BP	GO:0007064	mitotic sister chromatid cohesion	9	31	3.780e-02
GO:BP	GO:0045010	actin nucleation	14	62	3.780e-02
GO:BP	GO:0016226	iron-sulfur cluster assembly	9	31	3.780e-02
GO:BP	GO:0031163	metallo-sulfur cluster assembly	9	31	3.780e-02
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	11	43	3.866e-02
GO:BP	GO:0032970	regulation of actin filament-based process	54	376	3.866e-02
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	23	126	3.879e-02
GO:BP	GO:1900225	regulation of NLRP3 inflammasome complex assembly	10	37	3.880e-02
GO:BP	GO:0006753	nucleoside phosphate metabolic process	85	646	3.880e-02
GO:BP	GO:0016925	protein sumoylation	15	69	3.887e-02
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	42	276	3.887e-02
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	88	673	3.894e-02
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	19	97	3.929e-02
GO:BP	GO:0097581	lamellipodium organization	18	90	3.979e-02
GO:BP	GO:0019827	stem cell population maintenance	30	180	3.985e-02
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	14	63	4.209e-02
GO:BP	GO:0071044	histone mRNA catabolic process	5	11	4.209e-02
GO:BP	GO:0018195	peptidyl-arginine modification	5	11	4.209e-02
GO:BP	GO:0042255	ribosome assembly	14	63	4.209e-02
GO:BP	GO:0046048	UDP metabolic process	4	7	4.209e-02
GO:BP	GO:0031167	rRNA methylation	8	26	4.209e-02
GO:BP	GO:0150093	amyloid-beta clearance by transcytosis	4	7	4.209e-02
GO:BP	GO:0170036	import into the mitochondrion	12	50	4.209e-02
GO:BP	GO:0035601	protein deacylation	12	50	4.209e-02
GO:BP	GO:0035617	stress granule disassembly	4	7	4.209e-02
GO:BP	GO:0043488	regulation of mRNA stability	30	181	4.209e-02
GO:BP	GO:0009193	pyrimidine ribonucleoside diphosphate metabolic process	4	7	4.209e-02
GO:BP	GO:0051204	protein insertion into mitochondrial membrane	4	7	4.209e-02
GO:BP	GO:0033617	mitochondrial cytochrome c oxidase assembly	8	26	4.209e-02
GO:BP	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	10	38	4.590e-02
GO:BP	GO:0090043	regulation of tubulin deacetylation	7	21	4.664e-02
GO:BP	GO:0099188	postsynaptic cytoskeleton organization	7	21	4.664e-02
GO:BP	GO:0030162	regulation of proteolysis	57	406	4.664e-02
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	24	136	4.690e-02
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	24	136	4.690e-02
GO:BP	GO:0009261	ribonucleotide catabolic process	24	136	4.690e-02
GO:BP	GO:0009117	nucleotide metabolic process	67	493	4.717e-02
GO:BP	GO:1900034	regulation of cellular response to heat	6	16	4.717e-02
GO:BP	GO:0046036	CTP metabolic process	6	16	4.717e-02
GO:BP	GO:0098974	postsynaptic actin cytoskeleton organization	6	16	4.717e-02
GO:BP	GO:0002218	activation of innate immune response	45	305	4.776e-02
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	37	239	4.778e-02
GO:BP	GO:0000018	regulation of DNA recombination	25	144	4.793e-02
GO:BP	GO:0030032	lamellipodium assembly	15	71	4.838e-02
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	155	1296	4.962e-02
KEGG	KEGG:05168	Herpes simplex virus 1 infection	105	506	2.196e-09
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	35	140	1.825e-04
KEGG	KEGG:03082	ATP-dependent chromatin remodeling	30	116	3.337e-04
KEGG	KEGG:03040	Spliceosome	39	174	4.202e-04
KEGG	KEGG:03018	RNA degradation	22	79	1.166e-03
KEGG	KEGG:00970	Aminoacyl-tRNA biosynthesis	15	44	1.572e-03
KEGG	KEGG:03008	Ribosome biogenesis in eukaryotes	29	139	1.422e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	58	363	4.086e-02
KEGG	KEGG:04137	Mitophagy - animal	22	103	4.086e-02
KEGG	KEGG:04130	SNARE interactions in vesicular transport	10	32	4.368e-02
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	31	168	4.703e-02
KEGG	KEGG:04962	Vasopressin-regulated water reabsorption	12	44	4.703e-02

#write.csv(table_DOX24_down_genes, "output/table_DOX24_downreg_genes.csv")

#GO:BP
table_DOX24_down_genes_GOBP <- table_DOX24_down_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(table_motif1_GOBP_d, "data/table_motif1_GOBP_d.RDS")

table_DOX24_down_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific Down DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-5.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24_down_genes_KEGG <- table_DOX24_down_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24_down_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific Down DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-6.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX24T share Upregulated DEGs GO KEGG#####
D24Tshare_DEGs_up_mat <- as.matrix(DOX24Tshare_DEGs_GO_up)

DOX_24Tshare_up_dxr_gene <- gost(query = D24Tshare_DEGs_up_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24Tshare_up_gost_genes <- gostplot(DOX_24Tshare_up_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24Tshare_up_gost_genes

table_DOX24Tshare_up_genes <- DOX_24Tshare_up_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24Tshare_up_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	1318	5390	8.687e-45
GO:BP	GO:0048518	positive regulation of biological process	1482	6264	1.034e-43
GO:BP	GO:0048522	positive regulation of cellular process	1410	5920	1.664e-42
GO:BP	GO:0065007	biological regulation	2616	12743	2.240e-38
GO:BP	GO:0050789	regulation of biological process	2540	12336	8.310e-37
GO:BP	GO:0050794	regulation of cellular process	2470	11946	4.513e-36
GO:BP	GO:0035556	intracellular signal transduction	773	2965	5.621e-32
GO:BP	GO:0019538	protein metabolic process	1125	4721	3.115e-31
GO:BP	GO:0007275	multicellular organism development	1124	4727	8.277e-31
GO:BP	GO:0032502	developmental process	1474	6553	1.312e-30
GO:BP	GO:0009056	catabolic process	695	2639	1.032e-29
GO:BP	GO:0023051	regulation of signaling	865	3478	7.776e-29
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	967	3990	1.383e-28
GO:BP	GO:0019222	regulation of metabolic process	1553	7035	1.500e-28
GO:BP	GO:0048856	anatomical structure development	1356	5997	2.836e-28
GO:BP	GO:0051252	regulation of RNA metabolic process	904	3687	3.383e-28
GO:BP	GO:0010646	regulation of cell communication	863	3486	3.767e-28
GO:BP	GO:0051716	cellular response to stimulus	1608	7376	4.173e-27
GO:BP	GO:0050793	regulation of developmental process	643	2457	1.815e-26
GO:BP	GO:0009966	regulation of signal transduction	762	3034	3.203e-26
GO:BP	GO:0006351	DNA-templated transcription	863	3549	2.115e-25
GO:BP	GO:0048519	negative regulation of biological process	1308	5834	3.223e-25
GO:BP	GO:0048523	negative regulation of cellular process	1269	5629	3.223e-25
GO:BP	GO:0048583	regulation of response to stimulus	950	3993	4.200e-25
GO:BP	GO:0009893	positive regulation of metabolic process	871	3597	4.200e-25
GO:BP	GO:0051179	localization	1250	5555	2.251e-24
GO:BP	GO:0006355	regulation of DNA-templated transcription	829	3409	2.918e-24
GO:BP	GO:0048731	system development	957	4053	3.759e-24
GO:BP	GO:2001141	regulation of RNA biosynthetic process	830	3428	1.093e-23
GO:BP	GO:0030154	cell differentiation	1030	4437	1.112e-23
GO:BP	GO:0048869	cellular developmental process	1030	4438	1.174e-23
GO:BP	GO:0033554	cellular response to stress	497	1830	1.403e-23
GO:BP	GO:0006810	transport	1023	4407	1.677e-23
GO:BP	GO:0048468	cell development	714	2876	6.597e-23
GO:BP	GO:0051253	negative regulation of RNA metabolic process	398	1400	2.307e-22
GO:BP	GO:0036211	protein modification process	704	2846	4.431e-22
GO:BP	GO:0051239	regulation of multicellular organismal process	726	2956	5.427e-22
GO:BP	GO:0050896	response to stimulus	1872	8999	6.008e-22
GO:BP	GO:0043412	macromolecule modification	739	3030	1.410e-21
GO:BP	GO:0006796	phosphate-containing compound metabolic process	606	2407	1.928e-20
GO:BP	GO:0006793	phosphorus metabolic process	606	2410	2.597e-20
GO:BP	GO:0060255	regulation of macromolecule metabolic process	1402	6492	2.871e-20
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	418	1529	4.384e-20
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	363	1280	4.396e-20
GO:BP	GO:0006366	transcription by RNA polymerase II	664	2711	1.662e-19
GO:BP	GO:0010648	negative regulation of cell communication	395	1436	2.116e-19
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	364	1296	2.213e-19
GO:BP	GO:0048585	negative regulation of response to stimulus	447	1680	3.613e-19
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	635	2578	3.684e-19
GO:BP	GO:0023057	negative regulation of signaling	393	1435	5.869e-19
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	777	3288	7.089e-19
GO:BP	GO:0006950	response to stress	907	3948	8.496e-19
GO:BP	GO:0023052	signaling	1396	6515	9.974e-19
GO:BP	GO:0009968	negative regulation of signal transduction	368	1326	1.047e-18
GO:BP	GO:0045595	regulation of cell differentiation	422	1576	1.435e-18
GO:BP	GO:0032501	multicellular organismal process	1542	7322	3.081e-18
GO:BP	GO:0051641	cellular localization	847	3661	3.518e-18
GO:BP	GO:0051128	regulation of cellular component organization	600	2433	4.079e-18
GO:BP	GO:0009653	anatomical structure morphogenesis	657	2713	4.330e-18
GO:BP	GO:0007154	cell communication	1396	6540	4.632e-18
GO:BP	GO:0051234	establishment of localization	1091	4928	6.715e-18
GO:BP	GO:0009719	response to endogenous stimulus	400	1489	8.301e-18
GO:BP	GO:2000026	regulation of multicellular organismal development	384	1418	1.159e-17
GO:BP	GO:0071495	cellular response to endogenous stimulus	341	1223	1.290e-17
GO:BP	GO:0009894	regulation of catabolic process	300	1040	1.322e-17
GO:BP	GO:0008219	cell death	504	1991	3.372e-17
GO:BP	GO:0141124	intracellular signaling cassette	487	1912	4.219e-17
GO:BP	GO:0033036	macromolecule localization	755	3228	4.249e-17
GO:BP	GO:1902531	regulation of intracellular signal transduction	495	1953	5.560e-17
GO:BP	GO:0012501	programmed cell death	502	1987	5.784e-17
GO:BP	GO:0007165	signal transduction	1284	6002	2.228e-16
GO:BP	GO:0009889	regulation of biosynthetic process	1247	5809	2.917e-16
GO:BP	GO:0009057	macromolecule catabolic process	378	1417	2.992e-16
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	279	970	3.861e-16
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	508	2036	4.464e-16
GO:BP	GO:0051094	positive regulation of developmental process	361	1343	5.083e-16
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	271	938	6.198e-16
GO:BP	GO:0071363	cellular response to growth factor stimulus	213	689	8.698e-16
GO:BP	GO:0070848	response to growth factor	220	721	1.280e-15
GO:BP	GO:0051246	regulation of protein metabolic process	468	1855	1.340e-15
GO:BP	GO:0006915	apoptotic process	482	1923	1.448e-15
GO:BP	GO:0009891	positive regulation of biosynthetic process	638	2696	3.428e-15
GO:BP	GO:0022008	neurogenesis	448	1771	4.430e-15
GO:BP	GO:0070727	cellular macromolecule localization	654	2782	5.708e-15
GO:BP	GO:0051649	establishment of localization in cell	497	2010	6.104e-15
GO:BP	GO:0007399	nervous system development	618	2604	6.237e-15
GO:BP	GO:0008104	protein localization	651	2770	7.098e-15
GO:BP	GO:0051254	positive regulation of RNA metabolic process	460	1835	8.302e-15
GO:BP	GO:0071705	nitrogen compound transport	478	1923	9.447e-15
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	614	2593	1.289e-14
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1203	5644	1.864e-14
GO:BP	GO:0006996	organelle organization	811	3594	2.029e-14
GO:BP	GO:0032879	regulation of localization	498	2029	2.233e-14
GO:BP	GO:0046907	intracellular transport	362	1381	2.432e-14
GO:BP	GO:0042592	homeostatic process	436	1736	4.068e-14
GO:BP	GO:0007166	cell surface receptor signaling pathway	656	2819	4.707e-14
GO:BP	GO:0030030	cell projection organization	413	1631	6.661e-14
GO:BP	GO:0048513	animal organ development	707	3085	9.252e-14
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	425	1697	1.606e-13
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	425	1699	1.950e-13
GO:BP	GO:0043065	positive regulation of apoptotic process	167	528	2.858e-13
GO:BP	GO:0035295	tube development	297	1101	2.896e-13
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	400	1588	4.631e-13
GO:BP	GO:0048699	generation of neurons	389	1536	4.809e-13
GO:BP	GO:0016310	phosphorylation	343	1320	5.530e-13
GO:BP	GO:0015031	protein transport	369	1444	6.474e-13
GO:BP	GO:0043068	positive regulation of programmed cell death	170	546	7.479e-13
GO:BP	GO:0030182	neuron differentiation	370	1451	8.118e-13
GO:BP	GO:0043067	regulation of programmed cell death	381	1506	1.077e-12
GO:BP	GO:0051240	positive regulation of multicellular organismal process	414	1667	1.450e-12
GO:BP	GO:0042981	regulation of apoptotic process	371	1462	1.528e-12
GO:BP	GO:0061919	process utilizing autophagic mechanism	181	597	1.528e-12
GO:BP	GO:0006914	autophagy	181	597	1.528e-12
GO:BP	GO:0035239	tube morphogenesis	245	879	1.710e-12
GO:BP	GO:0010468	regulation of gene expression	1166	5536	2.953e-12
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	202	692	2.953e-12
GO:BP	GO:0009790	embryo development	300	1135	3.040e-12
GO:BP	GO:0006468	protein phosphorylation	319	1227	4.517e-12
GO:BP	GO:0009888	tissue development	486	2032	5.160e-12
GO:BP	GO:0070887	cellular response to chemical stimulus	518	2192	6.070e-12
GO:BP	GO:0051093	negative regulation of developmental process	253	925	6.103e-12
GO:BP	GO:0008283	cell population proliferation	482	2015	6.315e-12
GO:BP	GO:0043009	chordate embryonic development	196	671	6.315e-12
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	123	364	6.506e-12
GO:BP	GO:0065008	regulation of biological quality	668	2947	6.566e-12
GO:BP	GO:0031175	neuron projection development	274	1023	7.560e-12
GO:BP	GO:0048666	neuron development	307	1177	8.455e-12
GO:BP	GO:0060284	regulation of cell development	235	847	9.156e-12
GO:BP	GO:0006325	chromatin organization	243	884	1.021e-11
GO:BP	GO:0065009	regulation of molecular function	372	1496	2.644e-11
GO:BP	GO:0060562	epithelial tube morphogenesis	114	336	3.707e-11
GO:BP	GO:0009892	negative regulation of metabolic process	746	3375	4.505e-11
GO:BP	GO:0030163	protein catabolic process	272	1030	5.150e-11
GO:BP	GO:0016192	vesicle-mediated transport	390	1592	6.240e-11
GO:BP	GO:0016055	Wnt signaling pathway	143	458	6.649e-11
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	190	662	8.171e-11
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	319	1256	9.391e-11
GO:BP	GO:0048871	multicellular organismal-level homeostasis	226	825	1.046e-10
GO:BP	GO:0048732	gland development	141	454	1.455e-10
GO:BP	GO:0030097	hemopoiesis	258	976	1.777e-10
GO:BP	GO:0048584	positive regulation of response to stimulus	537	2331	1.787e-10
GO:BP	GO:0032880	regulation of protein localization	243	907	1.787e-10
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	114	344	1.960e-10
GO:BP	GO:0051049	regulation of transport	390	1607	2.335e-10
GO:BP	GO:0051241	negative regulation of multicellular organismal process	281	1087	2.669e-10
GO:BP	GO:0016236	macroautophagy	118	362	2.748e-10
GO:BP	GO:0043687	post-translational protein modification	268	1027	2.876e-10
GO:BP	GO:0060070	canonical Wnt signaling pathway	105	311	3.854e-10
GO:BP	GO:0060429	epithelium development	311	1238	6.887e-10
GO:BP	GO:0001701	in utero embryonic development	129	413	7.672e-10
GO:BP	GO:0060341	regulation of cellular localization	263	1013	8.091e-10
GO:BP	GO:0002009	morphogenesis of an epithelium	150	503	8.447e-10
GO:BP	GO:0045597	positive regulation of cell differentiation	234	879	8.566e-10
GO:BP	GO:0044238	primary metabolic process	2366	12342	9.418e-10
GO:BP	GO:0006338	chromatin remodeling	200	725	9.700e-10
GO:BP	GO:0032940	secretion by cell	228	854	1.155e-09
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	254	975	1.227e-09
GO:BP	GO:1901700	response to oxygen-containing compound	398	1669	1.607e-09
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	692	3157	1.883e-09
GO:BP	GO:0023056	positive regulation of signaling	423	1796	2.179e-09
GO:BP	GO:0001503	ossification	131	430	3.322e-09
GO:BP	GO:0009967	positive regulation of signal transduction	377	1578	4.395e-09
GO:BP	GO:0046903	secretion	255	992	4.660e-09
GO:BP	GO:0045596	negative regulation of cell differentiation	185	671	5.733e-09
GO:BP	GO:0040007	growth	241	929	6.130e-09
GO:BP	GO:0044281	small molecule metabolic process	416	1776	6.879e-09
GO:BP	GO:0000902	cell morphogenesis	255	996	7.015e-09
GO:BP	GO:0032446	protein modification by small protein conjugation	224	853	8.623e-09
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	178	643	8.956e-09
GO:BP	GO:0140352	export from cell	240	928	8.965e-09
GO:BP	GO:0080134	regulation of response to stress	336	1387	9.239e-09
GO:BP	GO:0010647	positive regulation of cell communication	419	1795	9.239e-09
GO:BP	GO:0030111	regulation of Wnt signaling pathway	106	331	9.257e-09
GO:BP	GO:0009890	negative regulation of biosynthetic process	620	2813	9.533e-09
GO:BP	GO:0009628	response to abiotic stimulus	285	1144	1.196e-08
GO:BP	GO:0042127	regulation of cell population proliferation	396	1685	1.238e-08
GO:BP	GO:0006629	lipid metabolic process	336	1391	1.284e-08
GO:BP	GO:0019941	modification-dependent protein catabolic process	176	638	1.459e-08
GO:BP	GO:0010506	regulation of autophagy	114	367	1.475e-08
GO:BP	GO:0070201	regulation of establishment of protein localization	153	537	1.832e-08
GO:BP	GO:0019637	organophosphate metabolic process	270	1077	1.832e-08
GO:BP	GO:0006508	proteolysis	354	1486	2.300e-08
GO:BP	GO:0001775	cell activation	281	1132	2.302e-08
GO:BP	GO:0097190	apoptotic signaling pathway	168	606	2.424e-08
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	217	831	2.630e-08
GO:BP	GO:0007033	vacuole organization	82	239	2.647e-08
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	207	786	3.059e-08
GO:BP	GO:0048762	mesenchymal cell differentiation	85	252	3.299e-08
GO:BP	GO:0006974	DNA damage response	233	908	3.299e-08
GO:BP	GO:0048729	tissue morphogenesis	169	614	3.756e-08
GO:BP	GO:0031344	regulation of cell projection organization	178	658	5.652e-08
GO:BP	GO:0051248	negative regulation of protein metabolic process	182	677	6.170e-08
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	85	255	6.200e-08
GO:BP	GO:0009896	positive regulation of catabolic process	153	546	6.200e-08
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	115	380	6.383e-08
GO:BP	GO:1901701	cellular response to oxygen-containing compound	289	1182	6.408e-08
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	174	642	7.261e-08
GO:BP	GO:0031399	regulation of protein modification process	261	1049	7.343e-08
GO:BP	GO:0045184	establishment of protein localization	441	1937	8.777e-08
GO:BP	GO:0048589	developmental growth	178	663	1.010e-07
GO:BP	GO:0060485	mesenchyme development	100	320	1.150e-07
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	170	628	1.209e-07
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	598	2745	1.338e-07
GO:BP	GO:0046649	lymphocyte activation	210	814	1.377e-07
GO:BP	GO:0016567	protein ubiquitination	200	768	1.479e-07
GO:BP	GO:0051130	positive regulation of cellular component organization	271	1105	1.516e-07
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	87	268	1.612e-07
GO:BP	GO:0001568	blood vessel development	192	732	1.665e-07
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	290	1199	1.807e-07
GO:BP	GO:0045321	leukocyte activation	244	980	2.290e-07
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	99	320	2.367e-07
GO:BP	GO:0040008	regulation of growth	163	604	3.123e-07
GO:BP	GO:1901698	response to nitrogen compound	264	1080	3.296e-07
GO:BP	GO:0001944	vasculature development	197	762	3.459e-07
GO:BP	GO:0050790	regulation of catalytic activity	232	928	3.746e-07
GO:BP	GO:0048754	branching morphogenesis of an epithelial tube	58	157	3.748e-07
GO:BP	GO:0016241	regulation of macroautophagy	65	184	3.813e-07
GO:BP	GO:0001525	angiogenesis	150	547	3.934e-07
GO:BP	GO:0006644	phospholipid metabolic process	115	392	4.100e-07
GO:BP	GO:0048863	stem cell differentiation	80	245	4.803e-07
GO:BP	GO:0010975	regulation of neuron projection development	127	446	5.013e-07
GO:BP	GO:1901699	cellular response to nitrogen compound	171	645	5.068e-07
GO:BP	GO:0045017	glycerolipid biosynthetic process	81	250	5.704e-07
GO:BP	GO:0001649	osteoblast differentiation	77	234	6.082e-07
GO:BP	GO:0044087	regulation of cellular component biogenesis	248	1011	6.605e-07
GO:BP	GO:0048608	reproductive structure development	96	314	7.284e-07
GO:BP	GO:0009725	response to hormone	226	907	7.507e-07
GO:BP	GO:1903829	positive regulation of protein localization	138	499	8.455e-07
GO:BP	GO:0048872	homeostasis of number of cells	100	332	8.473e-07
GO:BP	GO:0071559	response to transforming growth factor beta	85	269	8.984e-07
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	70	208	9.607e-07
GO:BP	GO:0046486	glycerolipid metabolic process	115	398	9.812e-07
GO:BP	GO:0045444	fat cell differentiation	78	241	1.066e-06
GO:BP	GO:0009267	cellular response to starvation	62	177	1.119e-06
GO:BP	GO:0048598	embryonic morphogenesis	164	620	1.134e-06
GO:BP	GO:0061138	morphogenesis of a branching epithelium	65	189	1.160e-06
GO:BP	GO:0016477	cell migration	353	1534	1.161e-06
GO:BP	GO:0051960	regulation of nervous system development	128	457	1.188e-06
GO:BP	GO:0006650	glycerophospholipid metabolic process	94	309	1.259e-06
GO:BP	GO:0050767	regulation of neurogenesis	110	378	1.259e-06
GO:BP	GO:0072359	circulatory system development	274	1145	1.259e-06
GO:BP	GO:0048514	blood vessel morphogenesis	167	635	1.259e-06
GO:BP	GO:0006979	response to oxidative stress	115	400	1.267e-06
GO:BP	GO:0061458	reproductive system development	96	318	1.348e-06
GO:BP	GO:0001501	skeletal system development	146	540	1.472e-06
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	165	629	1.806e-06
GO:BP	GO:0008285	negative regulation of cell population proliferation	181	706	2.352e-06
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	82	262	2.359e-06
GO:BP	GO:0000165	MAPK cascade	189	744	2.426e-06
GO:BP	GO:0002262	myeloid cell homeostasis	62	181	2.693e-06
GO:BP	GO:0045667	regulation of osteoblast differentiation	49	131	2.919e-06
GO:BP	GO:0001763	morphogenesis of a branching structure	68	206	3.272e-06
GO:BP	GO:0006886	intracellular protein transport	176	686	3.314e-06
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	94	315	3.314e-06
GO:BP	GO:0030099	myeloid cell differentiation	123	443	3.515e-06
GO:BP	GO:0019216	regulation of lipid metabolic process	95	320	3.671e-06
GO:BP	GO:0042594	response to starvation	71	219	3.760e-06
GO:BP	GO:0051338	regulation of transferase activity	135	498	3.857e-06
GO:BP	GO:0009887	animal organ morphogenesis	250	1042	3.857e-06
GO:BP	GO:0007049	cell cycle	375	1663	3.932e-06
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	93	312	3.977e-06
GO:BP	GO:0001837	epithelial to mesenchymal transition	59	171	3.977e-06
GO:BP	GO:0008654	phospholipid biosynthetic process	80	257	4.162e-06
GO:BP	GO:0010720	positive regulation of cell development	126	458	4.162e-06
GO:BP	GO:0051247	positive regulation of protein metabolic process	249	1039	4.423e-06
GO:BP	GO:0016032	viral process	118	423	4.674e-06
GO:BP	GO:0000045	autophagosome assembly	45	118	4.809e-06
GO:BP	GO:0051223	regulation of protein transport	122	442	5.360e-06
GO:BP	GO:0008610	lipid biosynthetic process	184	729	5.464e-06
GO:BP	GO:0042325	regulation of phosphorylation	205	830	6.019e-06
GO:BP	GO:0051174	regulation of phosphorus metabolic process	231	957	6.970e-06
GO:BP	GO:0046488	phosphatidylinositol metabolic process	56	162	7.476e-06
GO:BP	GO:1903311	regulation of mRNA metabolic process	92	312	7.693e-06
GO:BP	GO:0001889	liver development	52	147	8.720e-06
GO:BP	GO:0034101	erythrocyte homeostasis	52	147	8.720e-06
GO:BP	GO:0032868	response to insulin	82	270	8.923e-06
GO:BP	GO:0002682	regulation of immune system process	356	1581	9.394e-06
GO:BP	GO:0019220	regulation of phosphate metabolic process	230	956	9.505e-06
GO:BP	GO:0061448	connective tissue development	87	292	9.751e-06
GO:BP	GO:0002521	leukocyte differentiation	163	636	9.756e-06
GO:BP	GO:0044093	positive regulation of molecular function	215	884	9.978e-06
GO:BP	GO:0031400	negative regulation of protein modification process	100	349	1.024e-05
GO:BP	GO:0051604	protein maturation	142	539	1.049e-05
GO:BP	GO:1903706	regulation of hemopoiesis	117	425	1.054e-05
GO:BP	GO:0002062	chondrocyte differentiation	45	121	1.054e-05
GO:BP	GO:0042982	amyloid precursor protein metabolic process	32	74	1.083e-05
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	47	129	1.165e-05
GO:BP	GO:0016049	cell growth	130	485	1.177e-05
GO:BP	GO:0048870	cell motility	397	1793	1.177e-05
GO:BP	GO:0048858	cell projection morphogenesis	172	681	1.239e-05
GO:BP	GO:0043434	response to peptide hormone	120	440	1.246e-05
GO:BP	GO:0009987	cellular process	3634	20247	1.256e-05
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	38	96	1.365e-05
GO:BP	GO:0006259	DNA metabolic process	239	1005	1.387e-05
GO:BP	GO:0010628	positive regulation of gene expression	281	1212	1.390e-05
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	67	210	1.447e-05
GO:BP	GO:0009895	negative regulation of catabolic process	102	361	1.541e-05
GO:BP	GO:0062197	cellular response to chemical stress	92	317	1.541e-05
GO:BP	GO:0061013	regulation of mRNA catabolic process	64	198	1.541e-05
GO:BP	GO:0007417	central nervous system development	250	1061	1.609e-05
GO:BP	GO:1903131	mononuclear cell differentiation	140	534	1.614e-05
GO:BP	GO:0043534	blood vessel endothelial cell migration	44	119	1.624e-05
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	52	150	1.626e-05
GO:BP	GO:2000145	regulation of cell motility	242	1022	1.626e-05
GO:BP	GO:0061008	hepaticobiliary system development	52	150	1.626e-05
GO:BP	GO:0035282	segmentation	41	108	1.737e-05
GO:BP	GO:0032869	cellular response to insulin stimulus	66	207	1.743e-05
GO:BP	GO:0034504	protein localization to nucleus	92	318	1.744e-05
GO:BP	GO:1903530	regulation of secretion by cell	146	563	1.788e-05
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	170	676	1.824e-05
GO:BP	GO:0051129	negative regulation of cellular component organization	175	701	2.062e-05
GO:BP	GO:0061564	axon development	138	528	2.263e-05
GO:BP	GO:0006887	exocytosis	101	360	2.354e-05
GO:BP	GO:0005975	carbohydrate metabolic process	145	561	2.354e-05
GO:BP	GO:0030218	erythrocyte differentiation	48	136	2.354e-05
GO:BP	GO:0001932	regulation of protein phosphorylation	191	779	2.354e-05
GO:BP	GO:0072175	epithelial tube formation	48	136	2.354e-05
GO:BP	GO:1904951	positive regulation of establishment of protein localization	94	329	2.355e-05
GO:BP	GO:0030855	epithelial cell differentiation	184	746	2.446e-05
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	153	599	2.461e-05
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	52	152	2.465e-05
GO:BP	GO:0072163	mesonephric epithelium development	39	102	2.506e-05
GO:BP	GO:0072164	mesonephric tubule development	39	102	2.506e-05
GO:BP	GO:0051169	nuclear transport	95	334	2.511e-05
GO:BP	GO:0006913	nucleocytoplasmic transport	95	334	2.511e-05
GO:BP	GO:0001558	regulation of cell growth	111	406	2.662e-05
GO:BP	GO:1905037	autophagosome organization	45	125	2.671e-05
GO:BP	GO:0090407	organophosphate biosynthetic process	157	619	2.716e-05
GO:BP	GO:0032870	cellular response to hormone stimulus	161	638	2.740e-05
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	139	535	2.793e-05
GO:BP	GO:0001822	kidney development	92	322	2.959e-05
GO:BP	GO:0071453	cellular response to oxygen levels	55	165	2.972e-05
GO:BP	GO:0044088	regulation of vacuole organization	27	60	2.999e-05
GO:BP	GO:0060395	SMAD protein signal transduction	33	81	3.195e-05
GO:BP	GO:0034248	regulation of amide metabolic process	29	67	3.227e-05
GO:BP	GO:0043069	negative regulation of programmed cell death	216	905	3.396e-05
GO:BP	GO:0060674	placenta blood vessel development	18	32	3.417e-05
GO:BP	GO:0051726	regulation of cell cycle	253	1087	3.424e-05
GO:BP	GO:0022612	gland morphogenesis	46	130	3.424e-05
GO:BP	GO:0090183	regulation of kidney development	19	35	3.546e-05
GO:BP	GO:0048812	neuron projection morphogenesis	165	660	3.586e-05
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	49	142	3.587e-05
GO:BP	GO:0000302	response to reactive oxygen species	63	199	3.690e-05
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	258	1113	3.702e-05
GO:BP	GO:0006401	RNA catabolic process	90	315	3.714e-05
GO:BP	GO:0098657	import into cell	219	922	4.009e-05
GO:BP	GO:0030278	regulation of ossification	44	123	4.052e-05
GO:BP	GO:0046777	protein autophosphorylation	58	179	4.133e-05
GO:BP	GO:0071840	cellular component organization or biogenesis	1614	8393	4.147e-05
GO:BP	GO:0042221	response to chemical	795	3909	4.147e-05
GO:BP	GO:0043066	negative regulation of apoptotic process	209	874	4.216e-05
GO:BP	GO:1901652	response to peptide	227	962	4.216e-05
GO:BP	GO:0030879	mammary gland development	48	139	4.346e-05
GO:BP	GO:0034599	cellular response to oxidative stress	74	247	4.683e-05
GO:BP	GO:0040012	regulation of locomotion	248	1067	4.685e-05
GO:BP	GO:0045137	development of primary sexual characteristics	73	243	4.887e-05
GO:BP	GO:0001657	ureteric bud development	38	101	4.985e-05
GO:BP	GO:0035265	organ growth	54	164	5.291e-05
GO:BP	GO:0035148	tube formation	50	148	5.432e-05
GO:BP	GO:0031669	cellular response to nutrient levels	74	248	5.439e-05
GO:BP	GO:0006402	mRNA catabolic process	77	261	5.473e-05
GO:BP	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	19	36	5.882e-05
GO:BP	GO:0040011	locomotion	285	1255	5.960e-05
GO:BP	GO:0072001	renal system development	93	332	5.992e-05
GO:BP	GO:0010498	proteasomal protein catabolic process	139	543	6.057e-05
GO:BP	GO:0048638	regulation of developmental growth	88	310	6.137e-05
GO:BP	GO:0043603	amide metabolic process	120	455	6.285e-05
GO:BP	GO:0071773	cellular response to BMP stimulus	54	165	6.330e-05
GO:BP	GO:0071772	response to BMP	54	165	6.330e-05
GO:BP	GO:0018193	peptidyl-amino acid modification	169	686	6.433e-05
GO:BP	GO:0007423	sensory organ development	156	624	6.433e-05
GO:BP	GO:0045598	regulation of fat cell differentiation	46	133	6.451e-05
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	49	145	6.544e-05
GO:BP	GO:0001823	mesonephros development	39	106	6.671e-05
GO:BP	GO:0051640	organelle localization	155	620	6.855e-05
GO:BP	GO:0060348	bone development	67	220	7.239e-05
GO:BP	GO:0030334	regulation of cell migration	225	960	7.316e-05
GO:BP	GO:0007548	sex differentiation	84	294	7.585e-05
GO:BP	GO:0141188	nucleic acid catabolic process	95	343	7.638e-05
GO:BP	GO:0000278	mitotic cell cycle	211	892	7.720e-05
GO:BP	GO:0030509	BMP signaling pathway	51	154	7.883e-05
GO:BP	GO:0051046	regulation of secretion	154	617	7.998e-05
GO:BP	GO:0008152	metabolic process	2620	14136	8.156e-05
GO:BP	GO:0034097	response to cytokine	222	947	8.231e-05
GO:BP	GO:0008406	gonad development	71	238	8.231e-05
GO:BP	GO:0080135	regulation of cellular response to stress	133	519	8.905e-05
GO:BP	GO:0051216	cartilage development	65	213	9.142e-05
GO:BP	GO:1901135	carbohydrate derivative metabolic process	229	983	9.154e-05
GO:BP	GO:1903432	regulation of TORC1 signaling	36	96	9.311e-05
GO:BP	GO:0003006	developmental process involved in reproduction	240	1038	9.432e-05
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	64	209	9.432e-05
GO:BP	GO:0001838	embryonic epithelial tube formation	43	123	9.432e-05
GO:BP	GO:0048878	chemical homeostasis	241	1043	9.434e-05
GO:BP	GO:0033043	regulation of organelle organization	262	1148	9.684e-05
GO:BP	GO:0031345	negative regulation of cell projection organization	58	184	9.710e-05
GO:BP	GO:0098727	maintenance of cell number	58	184	9.710e-05
GO:BP	GO:0050673	epithelial cell proliferation	116	441	9.783e-05
GO:BP	GO:0043583	ear development	70	235	9.879e-05
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	110	414	1.048e-04
GO:BP	GO:0030098	lymphocyte differentiation	116	442	1.090e-04
GO:BP	GO:0010977	negative regulation of neuron projection development	45	132	1.192e-04
GO:BP	GO:0045926	negative regulation of growth	68	228	1.276e-04
GO:BP	GO:0050821	protein stabilization	67	224	1.338e-04
GO:BP	GO:0072210	metanephric nephron development	20	41	1.392e-04
GO:BP	GO:0048568	embryonic organ development	120	463	1.421e-04
GO:BP	GO:0036294	cellular response to decreased oxygen levels	49	149	1.430e-04
GO:BP	GO:0016197	endosomal transport	82	290	1.430e-04
GO:BP	GO:0007041	lysosomal transport	46	137	1.467e-04
GO:BP	GO:0051050	positive regulation of transport	200	847	1.474e-04
GO:BP	GO:0007034	vacuolar transport	55	174	1.507e-04
GO:BP	GO:0030308	negative regulation of cell growth	55	174	1.507e-04
GO:BP	GO:0044092	negative regulation of molecular function	139	553	1.514e-04
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	85	304	1.540e-04
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	85	304	1.540e-04
GO:BP	GO:0010638	positive regulation of organelle organization	126	492	1.542e-04
GO:BP	GO:0007267	cell-cell signaling	299	1342	1.546e-04
GO:BP	GO:0072073	kidney epithelium development	50	154	1.689e-04
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	68	230	1.704e-04
GO:BP	GO:0045637	regulation of myeloid cell differentiation	64	213	1.761e-04
GO:BP	GO:0044283	small molecule biosynthetic process	147	593	1.803e-04
GO:BP	GO:0042176	regulation of protein catabolic process	99	369	1.912e-04
GO:BP	GO:0045639	positive regulation of myeloid cell differentiation	37	103	2.019e-04
GO:BP	GO:0038202	TORC1 signaling	37	103	2.019e-04
GO:BP	GO:0019827	stem cell population maintenance	56	180	2.057e-04
GO:BP	GO:0009306	protein secretion	101	379	2.102e-04
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	20	42	2.102e-04
GO:BP	GO:0034614	cellular response to reactive oxygen species	48	147	2.104e-04
GO:BP	GO:0043487	regulation of RNA stability	59	193	2.165e-04
GO:BP	GO:0019752	carboxylic acid metabolic process	207	887	2.179e-04
GO:BP	GO:0007265	Ras protein signal transduction	42	123	2.182e-04
GO:BP	GO:0031667	response to nutrient levels	129	510	2.234e-04
GO:BP	GO:0002064	epithelial cell development	65	219	2.267e-04
GO:BP	GO:2001234	negative regulation of apoptotic signaling pathway	68	232	2.267e-04
GO:BP	GO:0072331	signal transduction by p53 class mediator	52	164	2.297e-04
GO:BP	GO:0043488	regulation of mRNA stability	56	181	2.408e-04
GO:BP	GO:0071345	cellular response to cytokine stimulus	200	854	2.408e-04
GO:BP	GO:0072273	metanephric nephron morphogenesis	14	24	2.412e-04
GO:BP	GO:0002428	antigen processing and presentation of peptide antigen via MHC class Ib	11	16	2.424e-04
GO:BP	GO:0001890	placenta development	49	152	2.448e-04
GO:BP	GO:0070482	response to oxygen levels	93	344	2.448e-04
GO:BP	GO:1905332	positive regulation of morphogenesis of an epithelium	18	36	2.448e-04
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	55	177	2.460e-04
GO:BP	GO:0031647	regulation of protein stability	91	335	2.460e-04
GO:BP	GO:0046395	carboxylic acid catabolic process	71	246	2.534e-04
GO:BP	GO:0016054	organic acid catabolic process	71	246	2.534e-04
GO:BP	GO:0042987	amyloid precursor protein catabolic process	24	56	2.534e-04
GO:BP	GO:0061053	somite development	32	85	2.538e-04
GO:BP	GO:0002063	chondrocyte development	17	33	2.539e-04
GO:BP	GO:0002040	sprouting angiogenesis	44	132	2.605e-04
GO:BP	GO:0007219	Notch signaling pathway	57	186	2.676e-04
GO:BP	GO:0022414	reproductive process	349	1608	2.733e-04
GO:BP	GO:0035592	establishment of protein localization to extracellular region	101	382	2.832e-04
GO:BP	GO:0010970	transport along microtubule	55	178	2.884e-04
GO:BP	GO:0042886	amide transport	90	332	2.923e-04
GO:BP	GO:0043542	endothelial cell migration	65	221	2.977e-04
GO:BP	GO:0006260	DNA replication	79	283	3.127e-04
GO:BP	GO:0045859	regulation of protein kinase activity	105	402	3.345e-04
GO:BP	GO:0051656	establishment of organelle localization	124	491	3.370e-04
GO:BP	GO:0007409	axonogenesis	118	463	3.454e-04
GO:BP	GO:0043436	oxoacid metabolic process	210	909	3.487e-04
GO:BP	GO:0009605	response to external stimulus	503	2415	3.567e-04
GO:BP	GO:0060322	head development	189	806	3.671e-04
GO:BP	GO:0042542	response to hydrogen peroxide	35	98	3.714e-04
GO:BP	GO:0043549	regulation of kinase activity	111	431	3.719e-04
GO:BP	GO:0006082	organic acid metabolic process	211	915	3.723e-04
GO:BP	GO:0050803	regulation of synapse structure or activity	86	316	3.748e-04
GO:BP	GO:0055088	lipid homeostasis	52	167	3.767e-04
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	36	102	3.768e-04
GO:BP	GO:2001235	positive regulation of apoptotic signaling pathway	45	138	3.768e-04
GO:BP	GO:0006643	membrane lipid metabolic process	63	214	3.768e-04
GO:BP	GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	13	22	3.881e-04
GO:BP	GO:0060603	mammary gland duct morphogenesis	17	34	4.025e-04
GO:BP	GO:0061180	mammary gland epithelium development	28	72	4.173e-04
GO:BP	GO:0030900	forebrain development	109	423	4.214e-04
GO:BP	GO:0016043	cellular component organization	1561	8184	4.253e-04
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	53	172	4.270e-04
GO:BP	GO:0030155	regulation of cell adhesion	186	794	4.412e-04
GO:BP	GO:0045646	regulation of erythrocyte differentiation	20	44	4.466e-04
GO:BP	GO:0060349	bone morphogenesis	36	103	4.715e-04
GO:BP	GO:0050807	regulation of synapse organization	84	309	4.748e-04
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	37	107	4.764e-04
GO:BP	GO:0030856	regulation of epithelial cell differentiation	49	156	4.891e-04
GO:BP	GO:0034612	response to tumor necrosis factor	66	229	4.948e-04
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	126	505	5.023e-04
GO:BP	GO:1905456	regulation of lymphoid progenitor cell differentiation	9	12	5.073e-04
GO:BP	GO:0042110	T cell activation	142	582	5.234e-04
GO:BP	GO:0030217	T cell differentiation	86	319	5.253e-04
GO:BP	GO:0071692	protein localization to extracellular region	101	388	5.253e-04
GO:BP	GO:0001892	embryonic placenta development	32	88	5.272e-04
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	46	144	5.272e-04
GO:BP	GO:0046890	regulation of lipid biosynthetic process	55	182	5.397e-04
GO:BP	GO:0071356	cellular response to tumor necrosis factor	61	208	5.524e-04
GO:BP	GO:0010508	positive regulation of autophagy	50	161	5.562e-04
GO:BP	GO:0060993	kidney morphogenesis	35	100	5.724e-04
GO:BP	GO:0008286	insulin receptor signaling pathway	41	124	5.771e-04
GO:BP	GO:0072088	nephron epithelium morphogenesis	30	81	6.175e-04
GO:BP	GO:0043276	anoikis	17	35	6.210e-04
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	83	307	6.332e-04
GO:BP	GO:0000209	protein polyubiquitination	77	280	6.443e-04
GO:BP	GO:0008284	positive regulation of cell population proliferation	217	954	6.626e-04
GO:BP	GO:1902117	positive regulation of organelle assembly	32	89	6.696e-04
GO:BP	GO:0043535	regulation of blood vessel endothelial cell migration	33	93	6.893e-04
GO:BP	GO:0002475	antigen processing and presentation via MHC class Ib	13	23	6.987e-04
GO:BP	GO:0060444	branching involved in mammary gland duct morphogenesis	13	23	6.987e-04
GO:BP	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	81	299	7.171e-04
GO:BP	GO:0061061	muscle structure development	164	693	7.227e-04
GO:BP	GO:1903053	regulation of extracellular matrix organization	25	63	7.227e-04
GO:BP	GO:0031929	TOR signaling	51	167	7.436e-04
GO:BP	GO:2000785	regulation of autophagosome assembly	21	49	7.825e-04
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	44	138	7.936e-04
GO:BP	GO:0050769	positive regulation of neurogenesis	69	246	8.088e-04
GO:BP	GO:0002484	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway	10	15	8.121e-04
GO:BP	GO:0002476	antigen processing and presentation of endogenous peptide antigen via MHC class Ib	10	15	8.121e-04
GO:BP	GO:0048864	stem cell development	31	86	8.155e-04
GO:BP	GO:0048511	rhythmic process	82	305	8.446e-04
GO:BP	GO:0007346	regulation of mitotic cell cycle	122	492	8.482e-04
GO:BP	GO:0051962	positive regulation of nervous system development	80	296	8.526e-04
GO:BP	GO:0042326	negative regulation of phosphorylation	72	260	8.641e-04
GO:BP	GO:0099111	microtubule-based transport	63	220	8.641e-04
GO:BP	GO:0050708	regulation of protein secretion	74	269	8.641e-04
GO:BP	GO:0007032	endosome organization	34	98	8.654e-04
GO:BP	GO:0061326	renal tubule development	36	106	8.708e-04
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	36	106	8.708e-04
GO:BP	GO:0010586	miRNA metabolic process	36	106	8.708e-04
GO:BP	GO:0072080	nephron tubule development	35	102	8.708e-04
GO:BP	GO:0060541	respiratory system development	64	225	9.315e-04
GO:BP	GO:0072006	nephron development	49	160	9.323e-04
GO:BP	GO:0021700	developmental maturation	92	352	9.323e-04
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	29	79	9.474e-04
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	48	156	9.673e-04
GO:BP	GO:0044282	small molecule catabolic process	96	371	9.724e-04
GO:BP	GO:0018209	peptidyl-serine modification	55	186	9.734e-04
GO:BP	GO:0072028	nephron morphogenesis	30	83	9.807e-04
GO:BP	GO:0097009	energy homeostasis	30	83	9.807e-04
GO:BP	GO:0016050	vesicle organization	97	376	1.000e-03
GO:BP	GO:0051168	nuclear export	51	169	1.000e-03
GO:BP	GO:0072087	renal vesicle development	11	18	1.015e-03
GO:BP	GO:0036293	response to decreased oxygen levels	84	316	1.015e-03
GO:BP	GO:0050435	amyloid-beta metabolic process	23	57	1.017e-03
GO:BP	GO:1902369	negative regulation of RNA catabolic process	32	91	1.029e-03
GO:BP	GO:0060999	positive regulation of dendritic spine development	19	43	1.032e-03
GO:BP	GO:0051259	protein complex oligomerization	74	271	1.080e-03
GO:BP	GO:0043010	camera-type eye development	94	363	1.100e-03
GO:BP	GO:0018105	peptidyl-serine phosphorylation	52	174	1.111e-03
GO:BP	GO:0007264	small GTPase-mediated signal transduction	124	505	1.113e-03
GO:BP	GO:0051898	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	24	61	1.129e-03
GO:BP	GO:0007420	brain development	175	754	1.148e-03
GO:BP	GO:0007042	lysosomal lumen acidification	13	24	1.171e-03
GO:BP	GO:0002320	lymphoid progenitor cell differentiation	13	24	1.171e-03
GO:BP	GO:0002483	antigen processing and presentation of endogenous peptide antigen	13	24	1.171e-03
GO:BP	GO:0014032	neural crest cell development	29	80	1.188e-03
GO:BP	GO:0034330	cell junction organization	191	834	1.190e-03
GO:BP	GO:0032259	methylation	66	236	1.201e-03
GO:BP	GO:0006606	protein import into nucleus	50	166	1.203e-03
GO:BP	GO:0031348	negative regulation of defense response	70	254	1.210e-03
GO:BP	GO:0061795	Golgi lumen acidification	9	13	1.211e-03
GO:BP	GO:0043408	regulation of MAPK cascade	151	637	1.217e-03
GO:BP	GO:0001843	neural tube closure	31	88	1.247e-03
GO:BP	GO:0032102	negative regulation of response to external stimulus	99	388	1.274e-03
GO:BP	GO:0006109	regulation of carbohydrate metabolic process	52	175	1.274e-03
GO:BP	GO:0005996	monosaccharide metabolic process	69	250	1.280e-03
GO:BP	GO:0051961	negative regulation of nervous system development	44	141	1.280e-03
GO:BP	GO:0048255	mRNA stabilization	26	69	1.301e-03
GO:BP	GO:0035329	hippo signaling	23	58	1.343e-03
GO:BP	GO:0051402	neuron apoptotic process	79	296	1.378e-03
GO:BP	GO:0061614	miRNA transcription	28	77	1.444e-03
GO:BP	GO:0034205	amyloid-beta formation	19	44	1.447e-03
GO:BP	GO:0006417	regulation of translation	97	380	1.455e-03
GO:BP	GO:1900180	regulation of protein localization to nucleus	45	146	1.460e-03
GO:BP	GO:0042063	gliogenesis	91	352	1.460e-03
GO:BP	GO:0031346	positive regulation of cell projection organization	92	357	1.511e-03
GO:BP	GO:0051147	regulation of muscle cell differentiation	44	142	1.511e-03
GO:BP	GO:0071456	cellular response to hypoxia	44	142	1.511e-03
GO:BP	GO:0071897	DNA biosynthetic process	51	172	1.540e-03
GO:BP	GO:0019080	viral gene expression	36	109	1.540e-03
GO:BP	GO:0060606	tube closure	31	89	1.540e-03
GO:BP	GO:0046620	regulation of organ growth	31	89	1.540e-03
GO:BP	GO:0006066	alcohol metabolic process	93	362	1.547e-03
GO:BP	GO:0044772	mitotic cell cycle phase transition	107	428	1.551e-03
GO:BP	GO:0090398	cellular senescence	34	101	1.555e-03
GO:BP	GO:0070301	cellular response to hydrogen peroxide	25	66	1.565e-03
GO:BP	GO:0071214	cellular response to abiotic stimulus	88	339	1.587e-03
GO:BP	GO:0104004	cellular response to environmental stimulus	88	339	1.587e-03
GO:BP	GO:0031347	regulation of defense response	185	809	1.589e-03
GO:BP	GO:0038066	p38MAPK cascade	22	55	1.589e-03
GO:BP	GO:0050768	negative regulation of neurogenesis	42	134	1.591e-03
GO:BP	GO:0090596	sensory organ morphogenesis	78	293	1.606e-03
GO:BP	GO:0007162	negative regulation of cell adhesion	78	293	1.606e-03
GO:BP	GO:0002520	immune system development	58	203	1.614e-03
GO:BP	GO:0072171	mesonephric tubule morphogenesis	26	70	1.642e-03
GO:BP	GO:0045669	positive regulation of osteoblast differentiation	26	70	1.642e-03
GO:BP	GO:0060443	mammary gland morphogenesis	20	48	1.652e-03
GO:BP	GO:0033365	protein localization to organelle	264	1209	1.652e-03
GO:BP	GO:0033993	response to lipid	209	930	1.652e-03
GO:BP	GO:0046466	membrane lipid catabolic process	20	48	1.652e-03
GO:BP	GO:0006623	protein targeting to vacuole	20	48	1.652e-03
GO:BP	GO:0032386	regulation of intracellular transport	72	266	1.659e-03
GO:BP	GO:0050865	regulation of cell activation	149	632	1.670e-03
GO:BP	GO:0043085	positive regulation of catalytic activity	133	554	1.670e-03
GO:BP	GO:0001654	eye development	104	415	1.692e-03
GO:BP	GO:0021915	neural tube development	48	160	1.717e-03
GO:BP	GO:0048839	inner ear development	59	208	1.721e-03
GO:BP	GO:0010256	endomembrane system organization	145	613	1.736e-03
GO:BP	GO:0071887	leukocyte apoptotic process	38	118	1.740e-03
GO:BP	GO:0043489	RNA stabilization	28	78	1.755e-03
GO:BP	GO:0030162	regulation of proteolysis	102	406	1.756e-03
GO:BP	GO:0046579	positive regulation of Ras protein signal transduction	11	19	1.790e-03
GO:BP	GO:0050679	positive regulation of epithelial cell proliferation	58	204	1.813e-03
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	35	106	1.828e-03
GO:BP	GO:0019218	regulation of steroid metabolic process	34	102	1.839e-03
GO:BP	GO:0044090	positive regulation of vacuole organization	13	25	1.839e-03
GO:BP	GO:0009065	glutamine family amino acid catabolic process	13	25	1.839e-03
GO:BP	GO:2000628	regulation of miRNA metabolic process	31	90	1.840e-03
GO:BP	GO:0033157	regulation of intracellular protein transport	46	152	1.846e-03
GO:BP	GO:0009299	mRNA transcription	21	52	1.846e-03
GO:BP	GO:0051222	positive regulation of protein transport	70	258	1.846e-03
GO:BP	GO:0006403	RNA localization	57	200	1.901e-03
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	19	45	1.917e-03
GO:BP	GO:0010817	regulation of hormone levels	133	556	1.917e-03
GO:BP	GO:0001756	somitogenesis	25	67	1.950e-03
GO:BP	GO:0007610	behavior	157	674	1.983e-03
GO:BP	GO:0046660	female sex differentiation	39	123	2.004e-03
GO:BP	GO:0043062	extracellular structure organization	85	328	2.068e-03
GO:BP	GO:0072078	nephron tubule morphogenesis	28	79	2.195e-03
GO:BP	GO:1903047	mitotic cell cycle process	171	745	2.231e-03
GO:BP	GO:0061333	renal tubule morphogenesis	29	83	2.234e-03
GO:BP	GO:0009615	response to virus	103	414	2.346e-03
GO:BP	GO:0062012	regulation of small molecule metabolic process	83	320	2.374e-03
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	24	64	2.390e-03
GO:BP	GO:0150063	visual system development	104	419	2.390e-03
GO:BP	GO:0072009	nephron epithelium development	39	124	2.393e-03
GO:BP	GO:0061024	membrane organization	186	821	2.393e-03
GO:BP	GO:0051170	import into nucleus	50	171	2.400e-03
GO:BP	GO:0140673	transcription elongation-coupled chromatin remodeling	7	9	2.442e-03
GO:BP	GO:0023061	signal release	121	501	2.459e-03
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	57	202	2.470e-03
GO:BP	GO:0042327	positive regulation of phosphorylation	122	506	2.486e-03
GO:BP	GO:0002486	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	9	14	2.487e-03
GO:BP	GO:0001666	response to hypoxia	79	302	2.487e-03
GO:BP	GO:0048002	antigen processing and presentation of peptide antigen	25	68	2.490e-03
GO:BP	GO:0048593	camera-type eye morphogenesis	42	137	2.528e-03
GO:BP	GO:2000036	regulation of stem cell population maintenance	26	72	2.591e-03
GO:BP	GO:0046661	male sex differentiation	51	176	2.611e-03
GO:BP	GO:1903532	positive regulation of secretion by cell	78	298	2.653e-03
GO:BP	GO:1902893	regulation of miRNA transcription	27	76	2.662e-03
GO:BP	GO:0051055	negative regulation of lipid biosynthetic process	22	57	2.676e-03
GO:BP	GO:0051452	intracellular pH reduction	22	57	2.676e-03
GO:BP	GO:0060537	muscle tissue development	106	430	2.676e-03
GO:BP	GO:0032006	regulation of TOR signaling	44	146	2.717e-03
GO:BP	GO:0010906	regulation of glucose metabolic process	32	96	2.732e-03
GO:BP	GO:0060173	limb development	55	194	2.733e-03
GO:BP	GO:0048736	appendage development	55	194	2.733e-03
GO:BP	GO:0070925	organelle assembly	230	1046	2.770e-03
GO:BP	GO:0044770	cell cycle phase transition	127	532	2.807e-03
GO:BP	GO:0044843	cell cycle G1/S phase transition	63	230	2.807e-03
GO:BP	GO:0034329	cell junction assembly	121	503	2.834e-03
GO:BP	GO:0048880	sensory system development	105	426	2.837e-03
GO:BP	GO:0034349	glial cell apoptotic process	10	17	2.895e-03
GO:BP	GO:0072077	renal vesicle morphogenesis	10	17	2.895e-03
GO:BP	GO:0030198	extracellular matrix organization	84	327	2.926e-03
GO:BP	GO:0048705	skeletal system morphogenesis	64	235	2.963e-03
GO:BP	GO:0099175	regulation of postsynapse organization	45	151	2.972e-03
GO:BP	GO:0019318	hexose metabolic process	62	226	2.972e-03
GO:BP	GO:0010721	negative regulation of cell development	71	267	2.972e-03
GO:BP	GO:0045682	regulation of epidermis development	24	65	2.972e-03
GO:BP	GO:0007035	vacuolar acidification	16	36	2.972e-03
GO:BP	GO:2000630	positive regulation of miRNA metabolic process	24	65	2.972e-03
GO:BP	GO:0044804	nucleophagy	12	23	2.972e-03
GO:BP	GO:1902003	regulation of amyloid-beta formation	16	36	2.972e-03
GO:BP	GO:0034249	negative regulation of amide metabolic process	12	23	2.972e-03
GO:BP	GO:0016237	microautophagy	12	23	2.972e-03
GO:BP	GO:0016242	negative regulation of macroautophagy	16	36	2.972e-03
GO:BP	GO:0046854	phosphatidylinositol phosphate biosynthetic process	24	65	2.972e-03
GO:BP	GO:0060392	negative regulation of SMAD protein signal transduction	12	23	2.972e-03
GO:BP	GO:0007040	lysosome organization	36	113	2.985e-03
GO:BP	GO:0080171	lytic vacuole organization	36	113	2.985e-03
GO:BP	GO:2000786	positive regulation of autophagosome assembly	11	20	2.996e-03
GO:BP	GO:0098739	import across plasma membrane	55	195	3.038e-03
GO:BP	GO:0014706	striated muscle tissue development	101	408	3.050e-03
GO:BP	GO:0099177	regulation of trans-synaptic signaling	123	514	3.056e-03
GO:BP	GO:0060675	ureteric bud morphogenesis	25	69	3.058e-03
GO:BP	GO:0006997	nucleus organization	44	147	3.066e-03
GO:BP	GO:0051896	regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	70	263	3.116e-03
GO:BP	GO:0043112	receptor metabolic process	26	73	3.148e-03
GO:BP	GO:0001841	neural tube formation	33	101	3.162e-03
GO:BP	GO:0060996	dendritic spine development	33	101	3.162e-03
GO:BP	GO:0071695	anatomical structure maturation	73	277	3.176e-03
GO:BP	GO:0001933	negative regulation of protein phosphorylation	66	245	3.198e-03
GO:BP	GO:0009880	embryonic pattern specification	27	77	3.198e-03
GO:BP	GO:0001656	metanephros development	31	93	3.225e-03
GO:BP	GO:0019915	lipid storage	31	93	3.225e-03
GO:BP	GO:0170062	nutrient storage	31	93	3.225e-03
GO:BP	GO:0044419	biological process involved in interspecies interaction between organisms	367	1759	3.280e-03
GO:BP	GO:0006575	modified amino acid metabolic process	51	178	3.280e-03
GO:BP	GO:0006839	mitochondrial transport	51	178	3.280e-03
GO:BP	GO:0045229	external encapsulating structure organization	84	329	3.443e-03
GO:BP	GO:0001658	branching involved in ureteric bud morphogenesis	23	62	3.564e-03
GO:BP	GO:0006457	protein folding	60	219	3.690e-03
GO:BP	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	24	66	3.730e-03
GO:BP	GO:0006897	endocytosis	162	709	3.730e-03
GO:BP	GO:0002376	immune system process	576	2871	3.741e-03
GO:BP	GO:0046578	regulation of Ras protein signal transduction	20	51	3.776e-03
GO:BP	GO:0008063	Toll signaling pathway	8	12	3.788e-03
GO:BP	GO:0015833	peptide transport	75	288	3.798e-03
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	14	30	3.820e-03
GO:BP	GO:0019725	cellular homeostasis	187	835	3.890e-03
GO:BP	GO:0072089	stem cell proliferation	38	123	3.891e-03
GO:BP	GO:0014020	primary neural tube formation	31	94	3.915e-03
GO:BP	GO:0050804	modulation of chemical synaptic transmission	122	513	4.059e-03
GO:BP	GO:0050678	regulation of epithelial cell proliferation	91	364	4.139e-03
GO:BP	GO:0031099	regeneration	56	202	4.143e-03
GO:BP	GO:0010821	regulation of mitochondrion organization	36	115	4.171e-03
GO:BP	GO:1902115	regulation of organelle assembly	63	234	4.329e-03
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	82	322	4.329e-03
GO:BP	GO:0061005	cell differentiation involved in kidney development	22	59	4.331e-03
GO:BP	GO:0045604	regulation of epidermal cell differentiation	22	59	4.331e-03
GO:BP	GO:0030282	bone mineralization	39	128	4.401e-03
GO:BP	GO:0006672	ceramide metabolic process	34	107	4.421e-03
GO:BP	GO:0051348	negative regulation of transferase activity	48	167	4.421e-03
GO:BP	GO:0003413	chondrocyte differentiation involved in endochondral bone morphogenesis	9	15	4.639e-03
GO:BP	GO:0034616	response to laminar fluid shear stress	9	15	4.639e-03
GO:BP	GO:0009798	axis specification	32	99	4.642e-03
GO:BP	GO:1902993	positive regulation of amyloid precursor protein catabolic process	12	24	4.650e-03
GO:BP	GO:0042254	ribosome biogenesis	82	323	4.744e-03
GO:BP	GO:0048592	eye morphogenesis	49	172	4.788e-03
GO:BP	GO:0014015	positive regulation of gliogenesis	25	71	4.788e-03
GO:BP	GO:0006536	glutamate metabolic process	15	34	4.815e-03
GO:BP	GO:0019882	antigen processing and presentation	36	116	4.914e-03
GO:BP	GO:0090189	regulation of branching involved in ureteric bud morphogenesis	11	21	4.914e-03
GO:BP	GO:0042113	B cell activation	74	286	4.927e-03
GO:BP	GO:0034727	piecemeal microautophagy of the nucleus	10	18	4.927e-03
GO:BP	GO:0090190	positive regulation of branching involved in ureteric bud morphogenesis	10	18	4.927e-03
GO:BP	GO:0010544	negative regulation of platelet activation	10	18	4.927e-03
GO:BP	GO:0022402	cell cycle process	273	1280	5.132e-03
GO:BP	GO:0046879	hormone secretion	82	324	5.189e-03
GO:BP	GO:0051098	regulation of binding	58	213	5.226e-03
GO:BP	GO:0010718	positive regulation of epithelial to mesenchymal transition	21	56	5.243e-03
GO:BP	GO:0051260	protein homooligomerization	56	204	5.243e-03
GO:BP	GO:0009410	response to xenobiotic stimulus	106	439	5.336e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	165	730	5.347e-03
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	33	104	5.376e-03
GO:BP	GO:0043124	negative regulation of canonical NF-kappaB signal transduction	22	60	5.506e-03
GO:BP	GO:0019883	antigen processing and presentation of endogenous antigen	14	31	5.523e-03
GO:BP	GO:0003338	metanephros morphogenesis	14	31	5.523e-03
GO:BP	GO:0097421	liver regeneration	14	31	5.523e-03
GO:BP	GO:0010001	glial cell differentiation	69	264	5.552e-03
GO:BP	GO:0050658	RNA transport	46	160	5.582e-03
GO:BP	GO:0050657	nucleic acid transport	46	160	5.582e-03
GO:BP	GO:0007005	mitochondrion organization	105	435	5.667e-03
GO:BP	GO:0072524	pyridine-containing compound metabolic process	48	169	5.712e-03
GO:BP	GO:0010594	regulation of endothelial cell migration	48	169	5.712e-03
GO:BP	GO:0042632	cholesterol homeostasis	30	92	5.719e-03
GO:BP	GO:0045995	regulation of embryonic development	30	92	5.719e-03
GO:BP	GO:0060052	neurofilament cytoskeleton organization	7	10	5.746e-03
GO:BP	GO:0032007	negative regulation of TOR signaling	24	68	5.746e-03
GO:BP	GO:2000739	regulation of mesenchymal stem cell differentiation	7	10	5.746e-03
GO:BP	GO:2000048	negative regulation of cell-cell adhesion mediated by cadherin	7	10	5.746e-03
GO:BP	GO:0001655	urogenital system development	24	68	5.746e-03
GO:BP	GO:0090184	positive regulation of kidney development	7	10	5.746e-03
GO:BP	GO:1902105	regulation of leukocyte differentiation	83	330	5.746e-03
GO:BP	GO:0099536	synaptic signaling	180	807	5.758e-03
GO:BP	GO:0016239	positive regulation of macroautophagy	29	88	5.758e-03
GO:BP	GO:0032101	regulation of response to external stimulus	234	1082	5.770e-03
GO:BP	GO:0022408	negative regulation of cell-cell adhesion	54	196	5.786e-03
GO:BP	GO:0008333	endosome to lysosome transport	25	72	5.786e-03
GO:BP	GO:0061035	regulation of cartilage development	25	72	5.786e-03
GO:BP	GO:0051101	regulation of DNA binding	25	72	5.786e-03
GO:BP	GO:0009914	hormone transport	84	335	5.807e-03
GO:BP	GO:0051028	mRNA transport	39	130	5.807e-03
GO:BP	GO:0030857	negative regulation of epithelial cell differentiation	19	49	5.807e-03
GO:BP	GO:0009063	amino acid catabolic process	35	113	5.817e-03
GO:BP	GO:0046165	alcohol biosynthetic process	42	143	5.831e-03
GO:BP	GO:0008584	male gonad development	44	152	6.085e-03
GO:BP	GO:0032330	regulation of chondrocyte differentiation	20	53	6.226e-03
GO:BP	GO:0045912	negative regulation of carbohydrate metabolic process	20	53	6.226e-03
GO:BP	GO:0051052	regulation of DNA metabolic process	118	500	6.341e-03
GO:BP	GO:1903034	regulation of response to wounding	48	170	6.392e-03
GO:BP	GO:0002790	peptide secretion	68	261	6.426e-03
GO:BP	GO:1902895	positive regulation of miRNA transcription	21	57	6.565e-03
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	36	118	6.607e-03
GO:BP	GO:0055092	sterol homeostasis	30	93	6.770e-03
GO:BP	GO:0014033	neural crest cell differentiation	30	93	6.770e-03
GO:BP	GO:0030323	respiratory tube development	55	202	6.892e-03
GO:BP	GO:0006006	glucose metabolic process	51	184	6.901e-03
GO:BP	GO:0072665	protein localization to vacuole	29	89	6.901e-03
GO:BP	GO:0038095	Fc-epsilon receptor signaling pathway	12	25	6.906e-03
GO:BP	GO:0046546	development of primary male sexual characteristics	44	153	6.973e-03
GO:BP	GO:0042149	cellular response to glucose starvation	18	46	7.015e-03
GO:BP	GO:0016485	protein processing	60	225	7.028e-03
GO:BP	GO:0009952	anterior/posterior pattern specification	60	225	7.028e-03
GO:BP	GO:0060411	cardiac septum morphogenesis	24	69	7.059e-03
GO:BP	GO:0031397	negative regulation of protein ubiquitination	26	77	7.105e-03
GO:BP	GO:0050890	cognition	82	328	7.235e-03
GO:BP	GO:0038203	TORC2 signaling	8	13	7.346e-03
GO:BP	GO:0034111	negative regulation of homotypic cell-cell adhesion	8	13	7.346e-03
GO:BP	GO:0014013	regulation of gliogenesis	33	106	7.346e-03
GO:BP	GO:0032042	mitochondrial DNA metabolic process	11	22	7.530e-03
GO:BP	GO:0060038	cardiac muscle cell proliferation	19	50	7.530e-03
GO:BP	GO:0061709	reticulophagy	11	22	7.530e-03
GO:BP	GO:0003018	vascular process in circulatory system	70	272	7.548e-03
GO:BP	GO:0046627	negative regulation of insulin receptor signaling pathway	16	39	7.548e-03
GO:BP	GO:0001667	ameboidal-type cell migration	62	235	7.625e-03
GO:BP	GO:0060966	regulation of gene silencing by regulatory ncRNA	14	32	7.625e-03
GO:BP	GO:0035751	regulation of lysosomal lumen pH	14	32	7.625e-03
GO:BP	GO:0001659	temperature homeostasis	51	185	7.717e-03
GO:BP	GO:0002684	positive regulation of immune system process	236	1099	7.847e-03
GO:BP	GO:0009084	glutamine family amino acid biosynthetic process	10	19	7.912e-03
GO:BP	GO:0006491	N-glycan processing	10	19	7.912e-03
GO:BP	GO:1904263	positive regulation of TORC1 signaling	20	54	7.912e-03
GO:BP	GO:0050771	negative regulation of axonogenesis	20	54	7.912e-03
GO:BP	GO:0060560	developmental growth involved in morphogenesis	63	240	7.912e-03
GO:BP	GO:0035627	ceramide transport	9	16	7.926e-03
GO:BP	GO:0002065	columnar/cuboidal epithelial cell differentiation	35	115	7.926e-03
GO:BP	GO:1901874	negative regulation of post-translational protein modification	30	94	7.956e-03
GO:BP	GO:0055085	transmembrane transport	328	1578	7.976e-03
GO:BP	GO:0051236	establishment of RNA localization	46	163	7.999e-03
GO:BP	GO:0009611	response to wounding	131	568	8.189e-03
GO:BP	GO:0050714	positive regulation of protein secretion	43	150	8.302e-03
GO:BP	GO:0032456	endocytic recycling	28	86	8.321e-03
GO:BP	GO:0030149	sphingolipid catabolic process	17	43	8.336e-03
GO:BP	GO:2000973	regulation of pro-B cell differentiation	6	8	8.348e-03
GO:BP	GO:0046984	regulation of hemoglobin biosynthetic process	6	8	8.348e-03
GO:BP	GO:0051148	negative regulation of muscle cell differentiation	22	62	8.385e-03
GO:BP	GO:0072666	establishment of protein localization to vacuole	23	66	8.530e-03
GO:BP	GO:0006665	sphingolipid metabolic process	47	168	8.560e-03
GO:BP	GO:0016042	lipid catabolic process	87	354	8.576e-03
GO:BP	GO:0043392	negative regulation of DNA binding	13	29	8.739e-03
GO:BP	GO:0034250	positive regulation of amide metabolic process	13	29	8.739e-03
GO:BP	GO:0009649	entrainment of circadian clock	13	29	8.739e-03
GO:BP	GO:0060964	regulation of miRNA-mediated gene silencing	13	29	8.739e-03
GO:BP	GO:0030072	peptide hormone secretion	66	255	8.744e-03
GO:BP	GO:0006275	regulation of DNA replication	36	120	8.783e-03
GO:BP	GO:0009411	response to UV	44	155	8.896e-03
GO:BP	GO:0045055	regulated exocytosis	61	232	8.896e-03
GO:BP	GO:0042770	signal transduction in response to DNA damage	48	173	9.105e-03
GO:BP	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	31	99	9.105e-03
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	30	95	9.409e-03
GO:BP	GO:0048640	negative regulation of developmental growth	30	95	9.409e-03
GO:BP	GO:0099537	trans-synaptic signaling	173	781	9.422e-03
GO:BP	GO:0006261	DNA-templated DNA replication	45	160	9.579e-03
GO:BP	GO:0051047	positive regulation of secretion	80	322	9.647e-03
GO:BP	GO:0043484	regulation of RNA splicing	51	187	9.647e-03
GO:BP	GO:0006405	RNA export from nucleus	29	91	9.657e-03
GO:BP	GO:0002694	regulation of leukocyte activation	132	576	9.892e-03
GO:BP	GO:0002042	cell migration involved in sprouting angiogenesis	20	55	9.946e-03
GO:BP	GO:1900077	negative regulation of cellular response to insulin stimulus	16	40	9.970e-03
GO:BP	GO:0070227	lymphocyte apoptotic process	27	83	1.013e-02
GO:BP	GO:0002181	cytoplasmic translation	46	165	1.023e-02
GO:BP	GO:0061462	protein localization to lysosome	21	59	1.023e-02
GO:BP	GO:1901342	regulation of vasculature development	75	299	1.028e-02
GO:BP	GO:0006360	transcription by RNA polymerase I	24	71	1.049e-02
GO:BP	GO:0045600	positive regulation of fat cell differentiation	23	67	1.049e-02
GO:BP	GO:0001934	positive regulation of protein phosphorylation	113	483	1.051e-02
GO:BP	GO:0031401	positive regulation of protein modification process	144	637	1.058e-02
GO:BP	GO:0006658	phosphatidylserine metabolic process	11	23	1.133e-02
GO:BP	GO:0072202	cell differentiation involved in metanephros development	11	23	1.133e-02
GO:BP	GO:0046985	positive regulation of hemoglobin biosynthetic process	5	6	1.141e-02
GO:BP	GO:1904760	regulation of myofibroblast differentiation	5	6	1.141e-02
GO:BP	GO:2000354	regulation of ovarian follicle development	5	6	1.141e-02
GO:BP	GO:0022407	regulation of cell-cell adhesion	115	494	1.141e-02
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	52	193	1.141e-02
GO:BP	GO:0042270	protection from natural killer cell mediated cytotoxicity	5	6	1.141e-02
GO:BP	GO:1903708	positive regulation of hemopoiesis	52	193	1.141e-02
GO:BP	GO:0030522	intracellular receptor signaling pathway	91	377	1.155e-02
GO:BP	GO:0007254	JNK cascade	48	175	1.155e-02
GO:BP	GO:1902459	positive regulation of stem cell population maintenance	18	48	1.156e-02
GO:BP	GO:0006458	‘de novo’ protein folding	18	48	1.156e-02
GO:BP	GO:0007268	chemical synaptic transmission	171	775	1.167e-02
GO:BP	GO:1904238	pericyte cell differentiation	7	11	1.167e-02
GO:BP	GO:0035871	protein K11-linked deubiquitination	7	11	1.167e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	171	775	1.167e-02
GO:BP	GO:0090331	negative regulation of platelet aggregation	7	11	1.167e-02
GO:BP	GO:0072497	mesenchymal stem cell differentiation	7	11	1.167e-02
GO:BP	GO:0030324	lung development	53	198	1.186e-02
GO:BP	GO:0002067	glandular epithelial cell differentiation	15	37	1.186e-02
GO:BP	GO:0097300	programmed necrotic cell death	19	52	1.202e-02
GO:BP	GO:1990823	response to leukemia inhibitory factor	32	105	1.202e-02
GO:BP	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	32	105	1.202e-02
GO:BP	GO:0050866	negative regulation of cell activation	56	212	1.215e-02
GO:BP	GO:1900368	regulation of post-transcriptional gene silencing by regulatory ncRNA	13	30	1.219e-02
GO:BP	GO:0000002	mitochondrial genome maintenance	13	30	1.219e-02
GO:BP	GO:0006537	glutamate biosynthetic process	4	4	1.224e-02
GO:BP	GO:0035914	skeletal muscle cell differentiation	26	80	1.224e-02
GO:BP	GO:1990170	stress response to cadmium ion	4	4	1.224e-02
GO:BP	GO:1904761	negative regulation of myofibroblast differentiation	4	4	1.224e-02
GO:BP	GO:0002477	antigen processing and presentation of exogenous peptide antigen via MHC class Ib	4	4	1.224e-02
GO:BP	GO:0071585	detoxification of cadmium ion	4	4	1.224e-02
GO:BP	GO:0010868	negative regulation of triglyceride biosynthetic process	4	4	1.224e-02
GO:BP	GO:0015693	magnesium ion transport	10	20	1.224e-02
GO:BP	GO:0051051	negative regulation of transport	98	412	1.226e-02
GO:BP	GO:0043536	positive regulation of blood vessel endothelial cell migration	20	56	1.226e-02
GO:BP	GO:1902903	regulation of supramolecular fiber organization	92	383	1.240e-02
GO:BP	GO:0008631	intrinsic apoptotic signaling pathway in response to oxidative stress	21	60	1.249e-02
GO:BP	GO:0051881	regulation of mitochondrial membrane potential	24	72	1.251e-02
GO:BP	GO:0043414	macromolecule methylation	37	127	1.268e-02
GO:BP	GO:0010976	positive regulation of neuron projection development	44	158	1.275e-02
GO:BP	GO:0044819	mitotic G1/S transition checkpoint signaling	8	14	1.279e-02
GO:BP	GO:1901653	cellular response to peptide	8	14	1.279e-02
GO:BP	GO:0007000	nucleolus organization	9	17	1.279e-02
GO:BP	GO:0048388	endosomal lumen acidification	8	14	1.279e-02
GO:BP	GO:0043117	positive regulation of vascular permeability	9	17	1.279e-02
GO:BP	GO:0009749	response to glucose	55	208	1.279e-02
GO:BP	GO:0140718	facultative heterochromatin formation	8	14	1.279e-02
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	16	41	1.280e-02
GO:BP	GO:0045746	negative regulation of Notch signaling pathway	16	41	1.280e-02
GO:BP	GO:0009612	response to mechanical stimulus	58	222	1.289e-02
GO:BP	GO:0060627	regulation of vesicle-mediated transport	122	531	1.292e-02
GO:BP	GO:0006281	DNA repair	140	621	1.307e-02
GO:BP	GO:0070555	response to interleukin-1	33	110	1.318e-02
GO:BP	GO:0010507	negative regulation of autophagy	29	93	1.318e-02
GO:BP	GO:0033673	negative regulation of kinase activity	41	145	1.323e-02
GO:BP	GO:0045765	regulation of angiogenesis	73	293	1.361e-02
GO:BP	GO:0070585	protein localization to mitochondrion	38	132	1.370e-02
GO:BP	GO:0061001	regulation of dendritic spine morphogenesis	17	45	1.372e-02
GO:BP	GO:0046434	organophosphate catabolic process	63	246	1.381e-02
GO:BP	GO:0099173	postsynapse organization	63	246	1.381e-02
GO:BP	GO:0034405	response to fluid shear stress	14	34	1.388e-02
GO:BP	GO:0035270	endocrine system development	40	141	1.399e-02
GO:BP	GO:0045732	positive regulation of protein catabolic process	55	209	1.408e-02
GO:BP	GO:0048534	hematopoietic or lymphoid organ development	31	102	1.436e-02
GO:BP	GO:0042551	neuron maturation	18	49	1.439e-02
GO:BP	GO:0051650	establishment of vesicle localization	53	200	1.440e-02
GO:BP	GO:0032200	telomere organization	51	191	1.470e-02
GO:BP	GO:0043523	regulation of neuron apoptotic process	62	242	1.475e-02
GO:BP	GO:0040029	epigenetic regulation of gene expression	74	299	1.515e-02
GO:BP	GO:0051648	vesicle localization	57	219	1.523e-02
GO:BP	GO:0006879	intracellular iron ion homeostasis	23	69	1.523e-02
GO:BP	GO:1905330	regulation of morphogenesis of an epithelium	22	65	1.525e-02
GO:BP	GO:0044344	cellular response to fibroblast growth factor stimulus	33	111	1.525e-02
GO:BP	GO:0035924	cellular response to vascular endothelial growth factor stimulus	22	65	1.525e-02
GO:BP	GO:0060998	regulation of dendritic spine development	21	61	1.525e-02
GO:BP	GO:0060350	endochondral bone morphogenesis	21	61	1.525e-02
GO:BP	GO:0030258	lipid modification	52	196	1.530e-02
GO:BP	GO:0016072	rRNA metabolic process	67	266	1.536e-02
GO:BP	GO:0030513	positive regulation of BMP signaling pathway	15	38	1.537e-02
GO:BP	GO:0051249	regulation of lymphocyte activation	117	509	1.537e-02
GO:BP	GO:0030641	regulation of cellular pH	29	94	1.543e-02
GO:BP	GO:0001817	regulation of cytokine production	171	781	1.553e-02
GO:BP	GO:0010595	positive regulation of endothelial cell migration	32	107	1.591e-02
GO:BP	GO:0015695	organic cation transport	35	120	1.591e-02
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	32	107	1.591e-02
GO:BP	GO:1904018	positive regulation of vasculature development	46	169	1.591e-02
GO:BP	GO:1901136	carbohydrate derivative catabolic process	65	257	1.591e-02
GO:BP	GO:0099003	vesicle-mediated transport in synapse	65	257	1.591e-02
GO:BP	GO:0051453	regulation of intracellular pH	28	90	1.593e-02
GO:BP	GO:1903321	negative regulation of protein modification by small protein conjugation or removal	28	90	1.593e-02
GO:BP	GO:0001816	cytokine production	172	787	1.622e-02
GO:BP	GO:0060147	regulation of post-transcriptional gene silencing	13	31	1.636e-02
GO:BP	GO:0098868	bone growth	13	31	1.636e-02
GO:BP	GO:0000578	embryonic axis specification	16	42	1.644e-02
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	127	560	1.644e-02
GO:BP	GO:0019953	sexual reproduction	237	1122	1.644e-02
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	127	560	1.644e-02
GO:BP	GO:1990830	cellular response to leukemia inhibitory factor	31	103	1.649e-02
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	31	103	1.649e-02
GO:BP	GO:0048562	embryonic organ morphogenesis	75	305	1.649e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	39	138	1.659e-02
GO:BP	GO:0050728	negative regulation of inflammatory response	45	165	1.678e-02
GO:BP	GO:0030073	insulin secretion	55	211	1.703e-02
GO:BP	GO:0048469	cell maturation	55	211	1.703e-02
GO:BP	GO:0006753	nucleoside phosphate metabolic process	144	646	1.703e-02
GO:BP	GO:0006364	rRNA processing	58	225	1.709e-02
GO:BP	GO:0051100	negative regulation of binding	30	99	1.718e-02
GO:BP	GO:0032787	monocarboxylic acid metabolic process	138	616	1.720e-02
GO:BP	GO:0032526	response to retinoic acid	33	112	1.736e-02
GO:BP	GO:1901655	cellular response to ketone	33	112	1.736e-02
GO:BP	GO:1901873	regulation of post-translational protein modification	62	244	1.750e-02
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	46	170	1.765e-02
GO:BP	GO:0042698	ovulation cycle	24	74	1.770e-02
GO:BP	GO:0071260	cellular response to mechanical stimulus	24	74	1.770e-02
GO:BP	GO:1903825	organic acid transmembrane transport	42	152	1.779e-02
GO:BP	GO:0045668	negative regulation of osteoblast differentiation	18	50	1.780e-02
GO:BP	GO:0035850	epithelial cell differentiation involved in kidney development	18	50	1.780e-02
GO:BP	GO:0019377	glycolipid catabolic process	10	21	1.782e-02
GO:BP	GO:0046514	ceramide catabolic process	10	21	1.782e-02
GO:BP	GO:0045586	regulation of gamma-delta T cell differentiation	6	9	1.785e-02
GO:BP	GO:0000183	rDNA heterochromatin formation	6	9	1.785e-02
GO:BP	GO:0060363	cranial suture morphogenesis	6	9	1.785e-02
GO:BP	GO:0097192	extrinsic apoptotic signaling pathway in absence of ligand	23	70	1.785e-02
GO:BP	GO:0048318	axial mesoderm development	6	9	1.785e-02
GO:BP	GO:0003418	growth plate cartilage chondrocyte differentiation	6	9	1.785e-02
GO:BP	GO:0006406	mRNA export from nucleus	23	70	1.785e-02
GO:BP	GO:0032922	circadian regulation of gene expression	23	70	1.785e-02
GO:BP	GO:0003279	cardiac septum development	32	108	1.799e-02
GO:BP	GO:0050775	positive regulation of dendrite morphogenesis	14	35	1.799e-02
GO:BP	GO:0046545	development of primary female sexual characteristics	32	108	1.799e-02
GO:BP	GO:0110110	positive regulation of animal organ morphogenesis	14	35	1.799e-02
GO:BP	GO:0006024	glycosaminoglycan biosynthetic process	14	35	1.799e-02
GO:BP	GO:0016486	peptide hormone processing	14	35	1.799e-02
GO:BP	GO:0030336	negative regulation of cell migration	72	292	1.812e-02
GO:BP	GO:0006383	transcription by RNA polymerase III	21	62	1.812e-02
GO:BP	GO:0043433	negative regulation of DNA-binding transcription factor activity	37	130	1.819e-02
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	149	673	1.835e-02
GO:BP	GO:0002573	myeloid leukocyte differentiation	61	240	1.835e-02
GO:BP	GO:0045766	positive regulation of angiogenesis	45	166	1.843e-02
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	39	139	1.843e-02
GO:BP	GO:0008585	female gonad development	31	104	1.875e-02
GO:BP	GO:0032801	receptor catabolic process	12	28	1.886e-02
GO:BP	GO:0030031	cell projection assembly	137	613	1.894e-02
GO:BP	GO:1990778	protein localization to cell periphery	87	365	1.898e-02
GO:BP	GO:0007519	skeletal muscle tissue development	48	180	1.906e-02
GO:BP	GO:0030326	embryonic limb morphogenesis	36	126	1.916e-02
GO:BP	GO:0035113	embryonic appendage morphogenesis	36	126	1.916e-02
GO:BP	GO:0006952	defense response	375	1853	1.923e-02
GO:BP	GO:0008593	regulation of Notch signaling pathway	30	100	1.933e-02
GO:BP	GO:2000027	regulation of animal organ morphogenesis	26	83	1.933e-02
GO:BP	GO:0090181	regulation of cholesterol metabolic process	15	39	1.933e-02
GO:BP	GO:1905038	regulation of membrane lipid metabolic process	9	18	1.933e-02
GO:BP	GO:1901606	alpha-amino acid catabolic process	30	100	1.933e-02
GO:BP	GO:0019362	pyridine nucleotide metabolic process	44	162	1.933e-02
GO:BP	GO:1902430	negative regulation of amyloid-beta formation	9	18	1.933e-02
GO:BP	GO:0140448	signaling receptor ligand precursor processing	15	39	1.933e-02
GO:BP	GO:0030279	negative regulation of ossification	15	39	1.933e-02
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	26	83	1.933e-02
GO:BP	GO:0046496	nicotinamide nucleotide metabolic process	44	162	1.933e-02
GO:BP	GO:0043691	reverse cholesterol transport	9	18	1.933e-02
GO:BP	GO:0048565	digestive tract development	38	135	1.933e-02
GO:BP	GO:0060538	skeletal muscle organ development	51	194	1.933e-02
GO:BP	GO:0060323	head morphogenesis	15	39	1.933e-02
GO:BP	GO:0001776	leukocyte homeostasis	33	113	1.934e-02
GO:BP	GO:0106106	cold-induced thermogenesis	42	153	1.940e-02
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	79	327	1.990e-02
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	133	594	1.992e-02
GO:BP	GO:0061723	glycophagy	7	12	1.999e-02
GO:BP	GO:0048505	regulation of timing of cell differentiation	7	12	1.999e-02
GO:BP	GO:0060379	cardiac muscle cell myoblast differentiation	7	12	1.999e-02
GO:BP	GO:0009746	response to hexose	55	213	1.999e-02
GO:BP	GO:0060148	positive regulation of post-transcriptional gene silencing	7	12	1.999e-02
GO:BP	GO:2000637	positive regulation of miRNA-mediated gene silencing	7	12	1.999e-02
GO:BP	GO:1900370	positive regulation of post-transcriptional gene silencing by RNA	7	12	1.999e-02
GO:BP	GO:0002328	pro-B cell differentiation	7	12	1.999e-02
GO:BP	GO:0048635	negative regulation of muscle organ development	7	12	1.999e-02
GO:BP	GO:1905671	regulation of lysosome organization	7	12	1.999e-02
GO:BP	GO:0048711	positive regulation of astrocyte differentiation	7	12	1.999e-02
GO:BP	GO:0043255	regulation of carbohydrate biosynthetic process	29	96	2.002e-02
GO:BP	GO:2000146	negative regulation of cell motility	75	308	2.008e-02
GO:BP	GO:0048709	oligodendrocyte differentiation	32	109	2.008e-02
GO:BP	GO:0016322	neuron remodeling	8	15	2.008e-02
GO:BP	GO:0021537	telencephalon development	70	284	2.008e-02
GO:BP	GO:0070243	regulation of thymocyte apoptotic process	8	15	2.008e-02
GO:BP	GO:0072595	maintenance of protein localization in organelle	16	43	2.008e-02
GO:BP	GO:0071496	cellular response to external stimulus	24	75	2.023e-02
GO:BP	GO:0043409	negative regulation of MAPK cascade	43	158	2.023e-02
GO:BP	GO:0030183	B cell differentiation	43	158	2.023e-02
GO:BP	GO:0017157	regulation of exocytosis	48	181	2.066e-02
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	23	71	2.071e-02
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	17	47	2.077e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	28	92	2.077e-02
GO:BP	GO:0042789	mRNA transcription by RNA polymerase II	17	47	2.077e-02
GO:BP	GO:0060711	labyrinthine layer development	17	47	2.077e-02
GO:BP	GO:0006509	membrane protein ectodomain proteolysis	17	47	2.077e-02
GO:BP	GO:1903955	positive regulation of protein targeting to mitochondrion	13	32	2.081e-02
GO:BP	GO:1902253	regulation of intrinsic apoptotic signaling pathway by p53 class mediator	13	32	2.081e-02
GO:BP	GO:0061036	positive regulation of cartilage development	13	32	2.081e-02
GO:BP	GO:0006622	protein targeting to lysosome	13	32	2.081e-02
GO:BP	GO:0002831	regulation of response to biotic stimulus	122	540	2.088e-02
GO:BP	GO:0002683	negative regulation of immune system process	117	515	2.088e-02
GO:BP	GO:0045927	positive regulation of growth	64	256	2.088e-02
GO:BP	GO:0000422	autophagy of mitochondrion	31	105	2.088e-02
GO:BP	GO:0030330	DNA damage response, signal transduction by p53 class mediator	18	51	2.107e-02
GO:BP	GO:0089718	amino acid import across plasma membrane	18	51	2.107e-02
GO:BP	GO:0046460	neutral lipid biosynthetic process	18	51	2.107e-02
GO:BP	GO:0046463	acylglycerol biosynthetic process	18	51	2.107e-02
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	61	242	2.116e-02
GO:BP	GO:0032608	interferon-beta production	20	59	2.123e-02
GO:BP	GO:0048286	lung alveolus development	19	55	2.123e-02
GO:BP	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	19	55	2.123e-02
GO:BP	GO:0072170	metanephric tubule development	11	25	2.123e-02
GO:BP	GO:0032648	regulation of interferon-beta production	20	59	2.123e-02
GO:BP	GO:0150104	transport across blood-brain barrier	27	88	2.125e-02
GO:BP	GO:0008203	cholesterol metabolic process	40	145	2.125e-02
GO:BP	GO:0010232	vascular transport	27	88	2.125e-02
GO:BP	GO:0097435	supramolecular fiber organization	185	861	2.164e-02
GO:BP	GO:0007155	cell adhesion	313	1530	2.230e-02
GO:BP	GO:0031960	response to corticosteroid	43	159	2.240e-02
GO:BP	GO:0051150	regulation of smooth muscle cell differentiation	14	36	2.265e-02
GO:BP	GO:0070306	lens fiber cell differentiation	14	36	2.265e-02
GO:BP	GO:1903749	positive regulation of establishment of protein localization to mitochondrion	14	36	2.265e-02
GO:BP	GO:0019395	fatty acid oxidation	32	110	2.275e-02
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	25	80	2.288e-02
GO:BP	GO:0030500	regulation of bone mineralization	25	80	2.288e-02
GO:BP	GO:2000736	regulation of stem cell differentiation	25	80	2.288e-02
GO:BP	GO:0002260	lymphocyte homeostasis	25	80	2.288e-02
GO:BP	GO:2000147	positive regulation of cell motility	131	587	2.294e-02
GO:BP	GO:0071774	response to fibroblast growth factor	34	119	2.339e-02
GO:BP	GO:0006635	fatty acid beta-oxidation	24	76	2.366e-02
GO:BP	GO:0048332	mesoderm morphogenesis	24	76	2.366e-02
GO:BP	GO:0035108	limb morphogenesis	42	155	2.375e-02
GO:BP	GO:0035107	appendage morphogenesis	42	155	2.375e-02
GO:BP	GO:0006664	glycolipid metabolic process	31	106	2.389e-02
GO:BP	GO:0055123	digestive system development	40	146	2.390e-02
GO:BP	GO:0048753	pigment granule organization	15	40	2.400e-02
GO:BP	GO:0060412	ventricular septum morphogenesis	15	40	2.400e-02
GO:BP	GO:0070266	necroptotic process	15	40	2.400e-02
GO:BP	GO:0071901	negative regulation of protein serine/threonine kinase activity	23	72	2.426e-02
GO:BP	GO:0038034	signal transduction in absence of ligand	23	72	2.426e-02
GO:BP	GO:0072207	metanephric epithelium development	12	29	2.445e-02
GO:BP	GO:0035493	SNARE complex assembly	10	22	2.445e-02
GO:BP	GO:0048679	regulation of axon regeneration	12	29	2.445e-02
GO:BP	GO:0002066	columnar/cuboidal epithelial cell development	12	29	2.445e-02
GO:BP	GO:0044342	type B pancreatic cell proliferation	12	29	2.445e-02
GO:BP	GO:0070935	3’-UTR-mediated mRNA stabilization	12	29	2.445e-02
GO:BP	GO:0060384	innervation	12	29	2.445e-02
GO:BP	GO:0007350	blastoderm segmentation	12	29	2.445e-02
GO:BP	GO:0007611	learning or memory	69	282	2.459e-02
GO:BP	GO:2000106	regulation of leukocyte apoptotic process	27	89	2.462e-02
GO:BP	GO:0035023	regulation of Rho protein signal transduction	27	89	2.462e-02
GO:BP	GO:0033077	T cell differentiation in thymus	27	89	2.462e-02
GO:BP	GO:0031100	animal organ regeneration	22	68	2.467e-02
GO:BP	GO:0016125	sterol metabolic process	43	160	2.468e-02
GO:BP	GO:0005976	polysaccharide metabolic process	30	102	2.481e-02
GO:BP	GO:0015914	phospholipid transport	30	102	2.481e-02
GO:BP	GO:0007369	gastrulation	51	197	2.489e-02
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	51	197	2.489e-02
GO:BP	GO:0120161	regulation of cold-induced thermogenesis	41	151	2.490e-02
GO:BP	GO:0006639	acylglycerol metabolic process	37	133	2.502e-02
GO:BP	GO:0046883	regulation of hormone secretion	66	268	2.520e-02
GO:BP	GO:0007292	female gamete generation	46	174	2.526e-02
GO:BP	GO:0120163	negative regulation of cold-induced thermogenesis	17	48	2.530e-02
GO:BP	GO:0070228	regulation of lymphocyte apoptotic process	20	60	2.541e-02
GO:BP	GO:0007517	muscle organ development	86	365	2.542e-02
GO:BP	GO:0040013	negative regulation of locomotion	78	326	2.543e-02
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	118	524	2.588e-02
GO:BP	GO:0033353	S-adenosylmethionine cycle	5	7	2.608e-02
GO:BP	GO:0072197	ureter morphogenesis	5	7	2.608e-02
GO:BP	GO:1905806	regulation of synapse pruning	5	7	2.608e-02
GO:BP	GO:2000638	regulation of SREBP signaling pathway	5	7	2.608e-02
GO:BP	GO:1902652	secondary alcohol metabolic process	42	156	2.610e-02
GO:BP	GO:0051092	positive regulation of NF-kappaB transcription factor activity	34	120	2.612e-02
GO:BP	GO:0099504	synaptic vesicle cycle	56	221	2.615e-02
GO:BP	GO:0007507	heart development	134	605	2.635e-02
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	133	600	2.642e-02
GO:BP	GO:0007498	mesoderm development	38	138	2.645e-02
GO:BP	GO:0042692	muscle cell differentiation	94	405	2.649e-02
GO:BP	GO:1990845	adaptive thermogenesis	45	170	2.678e-02
GO:BP	GO:0031116	positive regulation of microtubule polymerization	13	33	2.678e-02
GO:BP	GO:0030510	regulation of BMP signaling pathway	31	107	2.683e-02
GO:BP	GO:1903509	liposaccharide metabolic process	31	107	2.683e-02
GO:BP	GO:0009062	fatty acid catabolic process	31	107	2.683e-02
GO:BP	GO:0060221	retinal rod cell differentiation	9	19	2.726e-02
GO:BP	GO:0097401	synaptic vesicle lumen acidification	9	19	2.726e-02
GO:BP	GO:0060231	mesenchymal to epithelial transition	9	19	2.726e-02
GO:BP	GO:0009100	glycoprotein metabolic process	87	371	2.726e-02
GO:BP	GO:1902992	negative regulation of amyloid precursor protein catabolic process	9	19	2.726e-02
GO:BP	GO:1903830	magnesium ion transmembrane transport	9	19	2.726e-02
GO:BP	GO:1902004	positive regulation of amyloid-beta formation	9	19	2.726e-02
GO:BP	GO:0006354	DNA-templated transcription elongation	37	134	2.798e-02
GO:BP	GO:0006638	neutral lipid metabolic process	37	134	2.798e-02
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	59	236	2.799e-02
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	74	308	2.804e-02
GO:BP	GO:0072384	organelle transport along microtubule	27	90	2.824e-02
GO:BP	GO:0010639	negative regulation of organelle organization	83	352	2.839e-02
GO:BP	GO:0043254	regulation of protein-containing complex assembly	97	421	2.845e-02
GO:BP	GO:0044782	cilium organization	99	431	2.855e-02
GO:BP	GO:0010770	positive regulation of cell morphogenesis	14	37	2.855e-02
GO:BP	GO:2000737	negative regulation of stem cell differentiation	11	26	2.855e-02
GO:BP	GO:0033002	muscle cell proliferation	53	208	2.877e-02
GO:BP	GO:0030199	collagen fibril organization	22	69	2.898e-02
GO:BP	GO:0003013	circulatory system process	133	602	2.922e-02
GO:BP	GO:1905039	carboxylic acid transmembrane transport	40	148	2.931e-02
GO:BP	GO:0043648	dicarboxylic acid metabolic process	29	99	2.962e-02
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	36	130	2.962e-02
GO:BP	GO:0048814	regulation of dendrite morphogenesis	21	65	2.968e-02
GO:BP	GO:0051145	smooth muscle cell differentiation	21	65	2.968e-02
GO:BP	GO:0002931	response to ischemia	21	65	2.968e-02
GO:BP	GO:0010958	regulation of amino acid import across plasma membrane	8	16	3.023e-02
GO:BP	GO:1903789	regulation of amino acid transmembrane transport	8	16	3.023e-02
GO:BP	GO:0045651	positive regulation of macrophage differentiation	8	16	3.023e-02
GO:BP	GO:1901987	regulation of cell cycle phase transition	98	427	3.025e-02
GO:BP	GO:0070231	T cell apoptotic process	20	61	3.025e-02
GO:BP	GO:0042306	regulation of protein import into nucleus	20	61	3.025e-02
GO:BP	GO:0009314	response to radiation	100	437	3.034e-02
GO:BP	GO:0015931	nucleobase-containing compound transport	59	237	3.034e-02
GO:BP	GO:0097306	cellular response to alcohol	31	108	3.043e-02
GO:BP	GO:2000772	regulation of cellular senescence	16	45	3.044e-02
GO:BP	GO:0046622	positive regulation of organ growth	16	45	3.044e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	46	176	3.046e-02
GO:BP	GO:0007389	pattern specification process	108	477	3.046e-02
GO:BP	GO:0009064	glutamine family amino acid metabolic process	25	82	3.048e-02
GO:BP	GO:0040017	positive regulation of locomotion	133	603	3.051e-02
GO:BP	GO:0051607	defense response to virus	76	319	3.053e-02
GO:BP	GO:0060688	regulation of morphogenesis of a branching structure	18	53	3.062e-02
GO:BP	GO:0043114	regulation of vascular permeability	17	49	3.062e-02
GO:BP	GO:0019083	viral transcription	18	53	3.062e-02
GO:BP	GO:0006111	regulation of gluconeogenesis	17	49	3.062e-02
GO:BP	GO:0034198	cellular response to amino acid starvation	18	53	3.062e-02
GO:BP	GO:0061082	myeloid leukocyte cytokine production	17	49	3.062e-02
GO:BP	GO:0016358	dendrite development	60	242	3.067e-02
GO:BP	GO:1990700	nucleolar chromatin organization	6	10	3.119e-02
GO:BP	GO:0046643	regulation of gamma-delta T cell activation	6	10	3.119e-02
GO:BP	GO:1990416	cellular response to brain-derived neurotrophic factor stimulus	6	10	3.119e-02
GO:BP	GO:0036446	myofibroblast differentiation	6	10	3.119e-02
GO:BP	GO:0031214	biomineral tissue development	47	181	3.136e-02
GO:BP	GO:0032688	negative regulation of interferon-beta production	7	13	3.149e-02
GO:BP	GO:1903055	positive regulation of extracellular matrix organization	12	30	3.149e-02
GO:BP	GO:0031571	mitotic G1 DNA damage checkpoint signaling	7	13	3.149e-02
GO:BP	GO:0034144	negative regulation of toll-like receptor 4 signaling pathway	7	13	3.149e-02
GO:BP	GO:0048609	multicellular organismal reproductive process	210	1000	3.149e-02
GO:BP	GO:1902902	negative regulation of autophagosome assembly	7	13	3.149e-02
GO:BP	GO:0040034	regulation of development, heterochronic	7	13	3.149e-02
GO:BP	GO:0019076	viral release from host cell	12	30	3.149e-02
GO:BP	GO:0035891	exit from host cell	12	30	3.149e-02
GO:BP	GO:0006596	polyamine biosynthetic process	7	13	3.149e-02
GO:BP	GO:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	12	30	3.149e-02
GO:BP	GO:0070914	UV-damage excision repair	7	13	3.149e-02
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	119	533	3.149e-02
GO:BP	GO:1901605	alpha-amino acid metabolic process	54	214	3.165e-02
GO:BP	GO:0034762	regulation of transmembrane transport	101	443	3.171e-02
GO:BP	GO:0046364	monosaccharide biosynthetic process	27	91	3.190e-02
GO:BP	GO:0044272	sulfur compound biosynthetic process	40	149	3.197e-02
GO:BP	GO:0001707	mesoderm formation	23	74	3.243e-02
GO:BP	GO:0014855	striated muscle cell proliferation	23	74	3.243e-02
GO:BP	GO:0038061	non-canonical NF-kappaB signal transduction	34	122	3.254e-02
GO:BP	GO:0072234	metanephric nephron tubule development	10	23	3.296e-02
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	46	177	3.319e-02
GO:BP	GO:0045833	negative regulation of lipid metabolic process	29	100	3.325e-02
GO:BP	GO:0019319	hexose biosynthetic process	26	87	3.347e-02
GO:BP	GO:0098609	cell-cell adhesion	205	976	3.392e-02
GO:BP	GO:0120009	intermembrane lipid transfer	13	34	3.392e-02
GO:BP	GO:0001569	branching involved in blood vessel morphogenesis	13	34	3.392e-02
GO:BP	GO:0042476	odontogenesis	37	136	3.452e-02
GO:BP	GO:1903828	negative regulation of protein localization	54	215	3.465e-02
GO:BP	GO:0010565	regulation of ketone metabolic process	35	127	3.465e-02
GO:BP	GO:0045216	cell-cell junction organization	54	215	3.465e-02
GO:BP	GO:0008088	axo-dendritic transport	25	83	3.502e-02
GO:BP	GO:0008543	fibroblast growth factor receptor signaling pathway	25	83	3.502e-02
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	59	239	3.534e-02
GO:BP	GO:0033500	carbohydrate homeostasis	64	263	3.538e-02
GO:BP	GO:0034284	response to monosaccharide	55	220	3.544e-02
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	14	38	3.548e-02
GO:BP	GO:0010762	regulation of fibroblast migration	14	38	3.548e-02
GO:BP	GO:0060043	regulation of cardiac muscle cell proliferation	14	38	3.548e-02
GO:BP	GO:0002763	positive regulation of myeloid leukocyte differentiation	20	62	3.548e-02
GO:BP	GO:1902229	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	14	38	3.548e-02
GO:BP	GO:0042058	regulation of epidermal growth factor receptor signaling pathway	20	62	3.548e-02
GO:BP	GO:0046467	membrane lipid biosynthetic process	40	150	3.550e-02
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	40	150	3.550e-02
GO:BP	GO:0006885	regulation of pH	30	105	3.585e-02
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	56	225	3.605e-02
GO:BP	GO:0014009	glial cell proliferation	19	58	3.616e-02
GO:BP	GO:0050796	regulation of insulin secretion	46	178	3.645e-02
GO:BP	GO:0070232	regulation of T cell apoptotic process	15	42	3.645e-02
GO:BP	GO:0045022	early endosome to late endosome transport	15	42	3.645e-02
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	34	123	3.653e-02
GO:BP	GO:0045599	negative regulation of fat cell differentiation	18	54	3.661e-02
GO:BP	GO:0060324	face development	18	54	3.661e-02
GO:BP	GO:0010761	fibroblast migration	18	54	3.661e-02
GO:BP	GO:0051301	cell division	143	658	3.674e-02
GO:BP	GO:0045687	positive regulation of glial cell differentiation	16	46	3.681e-02
GO:BP	GO:0031124	mRNA 3’-end processing	16	46	3.681e-02
GO:BP	GO:0009957	epidermal cell fate specification	4	5	3.700e-02
GO:BP	GO:0071072	negative regulation of phospholipid biosynthetic process	4	5	3.700e-02
GO:BP	GO:0006113	fermentation	4	5	3.700e-02
GO:BP	GO:0003431	growth plate cartilage chondrocyte development	4	5	3.700e-02
GO:BP	GO:0070345	negative regulation of fat cell proliferation	4	5	3.700e-02
GO:BP	GO:0097500	receptor localization to non-motile cilium	4	5	3.700e-02
GO:BP	GO:0015818	isoleucine transport	4	5	3.700e-02
GO:BP	GO:1905908	positive regulation of amyloid fibril formation	4	5	3.700e-02
GO:BP	GO:1903801	L-leucine import across plasma membrane	4	5	3.700e-02
GO:BP	GO:0007386	compartment pattern specification	4	5	3.700e-02
GO:BP	GO:0051176	positive regulation of sulfur metabolic process	4	5	3.700e-02
GO:BP	GO:2000051	negative regulation of non-canonical Wnt signaling pathway	4	5	3.700e-02
GO:BP	GO:0030325	adrenal gland development	11	27	3.700e-02
GO:BP	GO:0007416	synapse assembly	63	259	3.700e-02
GO:BP	GO:0060740	prostate gland epithelium morphogenesis	11	27	3.700e-02
GO:BP	GO:0016188	synaptic vesicle maturation	11	27	3.700e-02
GO:BP	GO:0033119	negative regulation of RNA splicing	11	27	3.700e-02
GO:BP	GO:0009408	response to heat	29	101	3.728e-02
GO:BP	GO:0022411	cellular component disassembly	101	446	3.728e-02
GO:BP	GO:0043086	negative regulation of catalytic activity	70	293	3.733e-02
GO:BP	GO:0060716	labyrinthine layer blood vessel development	9	20	3.756e-02
GO:BP	GO:0007351	tripartite regional subdivision	9	20	3.756e-02
GO:BP	GO:0006684	sphingomyelin metabolic process	9	20	3.756e-02
GO:BP	GO:0048339	paraxial mesoderm development	9	20	3.756e-02
GO:BP	GO:0002755	MyD88-dependent toll-like receptor signaling pathway	9	20	3.756e-02
GO:BP	GO:0008595	anterior/posterior axis specification, embryo	9	20	3.756e-02
GO:BP	GO:0032332	positive regulation of chondrocyte differentiation	9	20	3.756e-02
GO:BP	GO:0051384	response to glucocorticoid	37	137	3.763e-02
GO:BP	GO:0071396	cellular response to lipid	134	613	3.781e-02
GO:BP	GO:0001824	blastocyst development	33	119	3.804e-02
GO:BP	GO:0009743	response to carbohydrate	60	245	3.804e-02
GO:BP	GO:0060041	retina development in camera-type eye	45	174	3.805e-02
GO:BP	GO:0009607	response to biotic stimulus	329	1634	3.860e-02
GO:BP	GO:0032835	glomerulus development	22	71	3.860e-02
GO:BP	GO:0045786	negative regulation of cell cycle	87	377	3.862e-02
GO:BP	GO:0050808	synapse organization	124	563	3.954e-02
GO:BP	GO:0051952	regulation of amine transport	25	84	3.960e-02
GO:BP	GO:0006094	gluconeogenesis	25	84	3.960e-02
GO:BP	GO:0071347	cellular response to interleukin-1	25	84	3.960e-02
GO:BP	GO:0019082	viral protein processing	12	31	4.021e-02
GO:BP	GO:0006506	GPI anchor biosynthetic process	12	31	4.021e-02
GO:BP	GO:0003206	cardiac chamber morphogenesis	34	124	4.039e-02
GO:BP	GO:0009117	nucleotide metabolic process	110	493	4.135e-02
GO:BP	GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway	20	63	4.142e-02
GO:BP	GO:0045580	regulation of T cell differentiation	48	189	4.185e-02
GO:BP	GO:0030335	positive regulation of cell migration	123	559	4.189e-02
GO:BP	GO:0042060	wound healing	98	433	4.191e-02
GO:BP	GO:0170033	L-amino acid metabolic process	45	175	4.210e-02
GO:BP	GO:0061157	mRNA destabilization	29	102	4.245e-02
GO:BP	GO:1901797	negative regulation of signal transduction by p53 class mediator	13	35	4.252e-02
GO:BP	GO:0045879	negative regulation of smoothened signaling pathway	13	35	4.252e-02
GO:BP	GO:0090497	mesenchymal cell migration	19	59	4.252e-02
GO:BP	GO:0045834	positive regulation of lipid metabolic process	35	129	4.262e-02
GO:BP	GO:0038127	ERBB signaling pathway	35	129	4.262e-02
GO:BP	GO:0055091	phospholipid homeostasis	8	17	4.321e-02
GO:BP	GO:2000696	regulation of epithelial cell differentiation involved in kidney development	8	17	4.321e-02
GO:BP	GO:0045778	positive regulation of ossification	18	55	4.348e-02
GO:BP	GO:0090049	regulation of cell migration involved in sprouting angiogenesis	14	39	4.385e-02
GO:BP	GO:0032438	melanosome organization	14	39	4.385e-02
GO:BP	GO:0045862	positive regulation of proteolysis	54	218	4.388e-02
GO:BP	GO:0030850	prostate gland development	17	51	4.401e-02
GO:BP	GO:0019058	viral life cycle	73	310	4.401e-02
GO:BP	GO:1990090	cellular response to nerve growth factor stimulus	17	51	4.401e-02
GO:BP	GO:0097066	response to thyroid hormone	10	24	4.401e-02
GO:BP	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	17	51	4.401e-02
GO:BP	GO:0098719	sodium ion import across plasma membrane	10	24	4.401e-02
GO:BP	GO:0045088	regulation of innate immune response	101	449	4.411e-02
GO:BP	GO:0006023	aminoglycan biosynthetic process	15	43	4.419e-02
GO:BP	GO:0071364	cellular response to epidermal growth factor stimulus	15	43	4.419e-02
GO:BP	GO:0045740	positive regulation of DNA replication	15	43	4.419e-02
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	15	43	4.419e-02
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	16	47	4.424e-02
GO:BP	GO:0061351	neural precursor cell proliferation	44	171	4.456e-02
GO:BP	GO:1900076	regulation of cellular response to insulin stimulus	22	72	4.505e-02
GO:BP	GO:0032606	type I interferon production	34	125	4.505e-02
GO:BP	GO:0032479	regulation of type I interferon production	34	125	4.505e-02
GO:BP	GO:0062014	negative regulation of small molecule metabolic process	30	107	4.509e-02
GO:BP	GO:0034440	lipid oxidation	32	116	4.525e-02
GO:BP	GO:0060748	tertiary branching involved in mammary gland duct morphogenesis	3	3	4.548e-02
GO:BP	GO:0019661	glucose catabolic process to lactate via pyruvate	3	3	4.548e-02
GO:BP	GO:0002051	osteoblast fate commitment	3	3	4.548e-02
GO:BP	GO:0035621	ER to Golgi ceramide transport	3	3	4.548e-02
GO:BP	GO:0033693	neurofilament bundle assembly	3	3	4.548e-02
GO:BP	GO:0071403	cellular response to high density lipoprotein particle stimulus	3	3	4.548e-02
GO:BP	GO:0035494	SNARE complex disassembly	3	3	4.548e-02
GO:BP	GO:0060759	regulation of response to cytokine stimulus	45	176	4.548e-02
GO:BP	GO:0019660	glycolytic fermentation	3	3	4.548e-02
GO:BP	GO:0140961	cellular detoxification of metal ion	3	3	4.548e-02
GO:BP	GO:1904023	regulation of glucose catabolic process to lactate via pyruvate	3	3	4.548e-02
GO:BP	GO:0098849	cellular detoxification of cadmium ion	3	3	4.548e-02
GO:BP	GO:1905532	regulation of L-leucine import across plasma membrane	3	3	4.548e-02
GO:BP	GO:1905952	regulation of lipid localization	42	162	4.548e-02
GO:BP	GO:1990637	response to prolactin	3	3	4.548e-02
GO:BP	GO:0099185	postsynaptic intermediate filament cytoskeleton organization	3	3	4.548e-02
GO:BP	GO:0051563	smooth endoplasmic reticulum calcium ion homeostasis	3	3	4.548e-02
GO:BP	GO:0042335	cuticle development	3	3	4.548e-02
GO:BP	GO:0007113	endomitotic cell cycle	3	3	4.548e-02
GO:BP	GO:0072034	renal vesicle induction	3	3	4.548e-02
GO:BP	GO:0019659	glucose catabolic process to lactate	3	3	4.548e-02
GO:BP	GO:2000367	regulation of acrosomal vesicle exocytosis	3	3	4.548e-02
GO:BP	GO:0009826	unidimensional cell growth	3	3	4.548e-02
GO:BP	GO:0097355	protein localization to heterochromatin	3	3	4.548e-02
GO:BP	GO:0042593	glucose homeostasis	63	262	4.548e-02
GO:BP	GO:0006163	purine nucleotide metabolic process	97	430	4.610e-02
GO:BP	GO:0009994	oocyte differentiation	21	68	4.611e-02
GO:BP	GO:0060021	roof of mouth development	27	94	4.627e-02
GO:BP	GO:0008637	apoptotic mitochondrial changes	29	103	4.718e-02
GO:BP	GO:0072283	metanephric renal vesicle morphogenesis	7	14	4.723e-02
GO:BP	GO:0035970	peptidyl-threonine dephosphorylation	7	14	4.723e-02
GO:BP	GO:0090153	regulation of sphingolipid biosynthetic process	7	14	4.723e-02
GO:BP	GO:0098814	spontaneous synaptic transmission	7	14	4.723e-02
GO:BP	GO:0036151	phosphatidylcholine acyl-chain remodeling	7	14	4.723e-02
GO:BP	GO:1901533	negative regulation of hematopoietic progenitor cell differentiation	7	14	4.723e-02
GO:BP	GO:0015803	branched-chain amino acid transport	7	14	4.723e-02
GO:BP	GO:0003416	endochondral bone growth	11	28	4.761e-02
GO:BP	GO:1901798	positive regulation of signal transduction by p53 class mediator	11	28	4.761e-02
GO:BP	GO:0033059	cellular pigmentation	20	64	4.764e-02
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	38	144	4.764e-02
GO:BP	GO:0048599	oocyte development	20	64	4.764e-02
GO:BP	GO:2000377	regulation of reactive oxygen species metabolic process	38	144	4.764e-02
GO:BP	GO:0043604	amide biosynthetic process	44	172	4.809e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	102	456	4.831e-02
GO:BP	GO:0003433	chondrocyte development involved in endochondral bone morphogenesis	5	8	4.839e-02
GO:BP	GO:1902746	regulation of lens fiber cell differentiation	5	8	4.839e-02
GO:BP	GO:0006538	glutamate catabolic process	5	8	4.839e-02
GO:BP	GO:0045647	negative regulation of erythrocyte differentiation	5	8	4.839e-02
GO:BP	GO:0032344	regulation of aldosterone metabolic process	5	8	4.839e-02
GO:BP	GO:0072033	renal vesicle formation	5	8	4.839e-02
GO:BP	GO:0032347	regulation of aldosterone biosynthetic process	5	8	4.839e-02
GO:BP	GO:0003223	ventricular compact myocardium morphogenesis	5	8	4.839e-02
GO:BP	GO:1904026	regulation of collagen fibril organization	5	8	4.839e-02
GO:BP	GO:0006290	pyrimidine dimer repair	5	8	4.839e-02
GO:BP	GO:0007422	peripheral nervous system development	26	90	4.839e-02
GO:BP	GO:0007623	circadian rhythm	52	210	4.839e-02
GO:BP	GO:1901888	regulation of cell junction assembly	63	263	4.855e-02
GO:BP	GO:0018107	peptidyl-threonine phosphorylation	23	77	4.881e-02
GO:BP	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	19	60	4.883e-02
GO:BP	GO:0002448	mast cell mediated immunity	19	60	4.883e-02
GO:BP	GO:0071168	protein localization to chromatin	19	60	4.883e-02
GO:BP	GO:0072329	monocarboxylic acid catabolic process	34	126	4.905e-02
GO:BP	GO:0002444	myeloid leukocyte mediated immunity	32	117	4.955e-02
GO:BP	GO:0072521	purine-containing compound metabolic process	123	563	4.955e-02
GO:BP	GO:0036075	replacement ossification	12	32	4.960e-02
GO:BP	GO:0070570	regulation of neuron projection regeneration	12	32	4.960e-02
GO:BP	GO:0001958	endochondral ossification	12	32	4.960e-02
GO:BP	GO:1900038	negative regulation of cellular response to hypoxia	6	11	4.960e-02
GO:BP	GO:0180046	GPI anchored protein biosynthesis	12	32	4.960e-02
GO:BP	GO:0045684	positive regulation of epidermis development	12	32	4.960e-02
GO:BP	GO:0060767	epithelial cell proliferation involved in prostate gland development	6	11	4.960e-02
GO:BP	GO:0045843	negative regulation of striated muscle tissue development	6	11	4.960e-02
GO:BP	GO:0006505	GPI anchor metabolic process	12	32	4.960e-02
GO:BP	GO:2000644	regulation of receptor catabolic process	6	11	4.960e-02
GO:BP	GO:0071108	protein K48-linked deubiquitination	12	32	4.960e-02
GO:BP	GO:0006954	inflammatory response	181	862	4.960e-02
GO:BP	GO:0060397	growth hormone receptor signaling pathway via JAK-STAT	6	11	4.960e-02
GO:BP	GO:0062098	regulation of programmed necrotic cell death	12	32	4.960e-02
GO:BP	GO:0031943	regulation of glucocorticoid metabolic process	6	11	4.960e-02
GO:BP	GO:0003337	mesenchymal to epithelial transition involved in metanephros morphogenesis	6	11	4.960e-02
GO:BP	GO:0010807	regulation of synaptic vesicle priming	6	11	4.960e-02
GO:BP	GO:1990928	response to amino acid starvation	18	56	4.976e-02
GO:BP	GO:0046328	regulation of JNK cascade	37	140	4.986e-02
KEGG	KEGG:04140	Autophagy - animal	65	165	3.285e-05
KEGG	KEGG:05169	Epstein-Barr virus infection	72	198	1.376e-04
KEGG	KEGG:05161	Hepatitis B	61	162	1.678e-04
KEGG	KEGG:04070	Phosphatidylinositol signaling system	39	97	1.723e-03
KEGG	KEGG:05210	Colorectal cancer	35	86	2.681e-03
KEGG	KEGG:04218	Cellular senescence	54	155	4.155e-03
KEGG	KEGG:04350	TGF-beta signaling pathway	40	107	4.155e-03
KEGG	KEGG:04550	Signaling pathways regulating pluripotency of stem cells	50	143	4.155e-03
KEGG	KEGG:05131	Shigellosis	78	246	4.155e-03
KEGG	KEGG:05212	Pancreatic cancer	31	76	4.155e-03
KEGG	KEGG:04115	p53 signaling pathway	30	74	4.653e-03
KEGG	KEGG:01522	Endocrine resistance	36	95	5.025e-03
KEGG	KEGG:05203	Viral carcinogenesis	64	201	8.161e-03
KEGG	KEGG:05120	Epithelial cell signaling in Helicobacter pylori infection	28	70	8.161e-03
KEGG	KEGG:04142	Lysosome	45	131	9.339e-03
KEGG	KEGG:05165	Human papillomavirus infection	96	330	1.101e-02
KEGG	KEGG:05223	Non-small cell lung cancer	28	72	1.116e-02
KEGG	KEGG:05226	Gastric cancer	49	148	1.160e-02
KEGG	KEGG:00562	Inositol phosphate metabolism	28	73	1.253e-02
KEGG	KEGG:04010	MAPK signaling pathway	88	301	1.253e-02
KEGG	KEGG:05200	Pathways in cancer	143	527	1.262e-02
KEGG	KEGG:04068	FoxO signaling pathway	44	131	1.262e-02
KEGG	KEGG:04150	mTOR signaling pathway	50	155	1.555e-02
KEGG	KEGG:05167	Kaposi sarcoma-associated herpesvirus infection	60	194	1.633e-02
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	66	218	1.651e-02
KEGG	KEGG:05017	Spinocerebellar ataxia	46	141	1.651e-02
KEGG	KEGG:04750	Inflammatory mediator regulation of TRP channels	34	98	2.094e-02
KEGG	KEGG:03083	Polycomb repressive complex	30	84	2.220e-02
KEGG	KEGG:04919	Thyroid hormone signaling pathway	40	121	2.274e-02
KEGG	KEGG:05221	Acute myeloid leukemia	25	67	2.439e-02
KEGG	KEGG:05162	Measles	44	138	2.664e-02
KEGG	KEGG:04934	Cushing syndrome	48	153	2.664e-02
KEGG	KEGG:04710	Circadian rhythm	15	34	2.664e-02
KEGG	KEGG:00600	Sphingolipid metabolism	21	54	2.664e-02
KEGG	KEGG:05215	Prostate cancer	33	97	2.702e-02
KEGG	KEGG:04935	Growth hormone synthesis, secretion and action	39	120	2.842e-02
KEGG	KEGG:05213	Endometrial cancer	22	58	2.842e-02
KEGG	KEGG:05224	Breast cancer	46	147	2.885e-02
KEGG	KEGG:00280	Valine, leucine and isoleucine degradation	19	48	2.894e-02
KEGG	KEGG:04137	Mitophagy - animal	34	103	3.573e-02
KEGG	KEGG:05217	Basal cell carcinoma	23	63	3.585e-02
KEGG	KEGG:04390	Hippo signaling pathway	48	157	3.585e-02
KEGG	KEGG:04360	Axon guidance	54	181	3.694e-02
KEGG	KEGG:04330	Notch signaling pathway	22	60	3.843e-02
KEGG	KEGG:05225	Hepatocellular carcinoma	50	166	3.847e-02
KEGG	KEGG:04912	GnRH signaling pathway	31	93	3.847e-02
KEGG	KEGG:05110	Vibrio cholerae infection	19	50	4.078e-02
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	27	79	4.290e-02
KEGG	KEGG:04668	TNF signaling pathway	36	113	4.355e-02
KEGG	KEGG:00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	10	21	4.750e-02

#write.csv(table_DOX24R_up_genes, "output/table_DOX24R_upreg_genes.csv")

#GO:BP
table_DOX24Tshare_up_genes_GOBP <- table_DOX24Tshare_up_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(table_motif1_GOBP_d, "data/table_motif1_GOBP_d.RDS")

table_DOX24Tshare_up_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared Up DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-8.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24Tshare_up_genes_KEGG <- table_DOX24Tshare_up_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24Tshare_up_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared Up DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-9.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX24R Downregulated DEGs GO KEGG#####
D24Tshare_DEGs_down_mat <- as.matrix(DOX24Tshare_DEGs_GO_down)

DOX_24Tshare_down_dxr_gene <- gost(query = D24Tshare_DEGs_down_mat,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

DOX_24Tshare_down_gost_genes <- gostplot(DOX_24Tshare_down_dxr_gene, capped = FALSE, interactive = TRUE)
DOX_24Tshare_down_gost_genes

table_DOX24Tshare_down_genes <- DOX_24Tshare_down_dxr_gene$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24Tshare_down_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006996	organelle organization	1110	3594	7.044e-70
GO:BP	GO:0080090	regulation of primary metabolic process	1421	5390	3.141e-44
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	1082	3990	2.874e-36
GO:BP	GO:0033043	regulation of organelle organization	404	1148	9.181e-35
GO:BP	GO:0019538	protein metabolic process	1226	4721	6.559e-33
GO:BP	GO:0043412	macromolecule modification	847	3030	9.423e-32
GO:BP	GO:0007049	cell cycle	522	1663	8.045e-31
GO:BP	GO:0000278	mitotic cell cycle	325	892	8.045e-31
GO:BP	GO:0140053	mitochondrial gene expression	104	168	1.292e-30
GO:BP	GO:1903047	mitotic cell cycle process	284	745	1.456e-30
GO:BP	GO:0051641	cellular localization	982	3661	1.755e-30
GO:BP	GO:0022402	cell cycle process	423	1280	7.396e-30
GO:BP	GO:0051252	regulation of RNA metabolic process	984	3687	1.039e-29
GO:BP	GO:0006351	DNA-templated transcription	948	3549	1.616e-28
GO:BP	GO:0051128	regulation of cellular component organization	694	2433	4.282e-28
GO:BP	GO:0051649	establishment of localization in cell	594	2010	7.886e-28
GO:BP	GO:0032543	mitochondrial translation	84	130	1.298e-26
GO:BP	GO:0070925	organelle assembly	352	1046	3.555e-26
GO:BP	GO:0051726	regulation of cell cycle	361	1087	1.084e-25
GO:BP	GO:2001141	regulation of RNA biosynthetic process	905	3428	3.848e-25
GO:BP	GO:0006355	regulation of DNA-templated transcription	900	3409	5.437e-25
GO:BP	GO:0065007	biological regulation	2779	12743	6.710e-25
GO:BP	GO:0050789	regulation of biological process	2700	12336	1.833e-24
GO:BP	GO:0048522	positive regulation of cellular process	1431	5920	3.987e-24
GO:BP	GO:0006399	tRNA metabolic process	110	210	4.400e-24
GO:BP	GO:0046907	intracellular transport	428	1381	7.648e-24
GO:BP	GO:0010564	regulation of cell cycle process	259	720	1.351e-23
GO:BP	GO:0006281	DNA repair	232	621	1.491e-23
GO:BP	GO:0006974	DNA damage response	307	908	4.118e-23
GO:BP	GO:0033554	cellular response to stress	532	1830	6.259e-23
GO:BP	GO:0033036	macromolecule localization	848	3228	1.217e-22
GO:BP	GO:0006259	DNA metabolic process	330	1005	1.519e-22
GO:BP	GO:0048518	positive regulation of biological process	1491	6264	2.280e-22
GO:BP	GO:0050794	regulation of cellular process	2612	11946	2.808e-22
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	859	3288	3.054e-22
GO:BP	GO:0036211	protein modification process	758	2846	1.330e-21
GO:BP	GO:0051276	chromosome organization	214	574	1.373e-21
GO:BP	GO:0007010	cytoskeleton organization	455	1529	1.528e-21
GO:BP	GO:0070727	cellular macromolecule localization	743	2782	1.743e-21
GO:BP	GO:0140014	mitotic nuclear division	128	282	5.779e-21
GO:BP	GO:0009056	catabolic process	708	2639	7.216e-21
GO:BP	GO:0008104	protein localization	737	2770	8.093e-21
GO:BP	GO:0000819	sister chromatid segregation	111	234	5.847e-20
GO:BP	GO:0006412	translation	250	727	8.368e-20
GO:BP	GO:0051179	localization	1328	5555	8.368e-20
GO:BP	GO:0009893	positive regulation of metabolic process	913	3597	9.276e-20
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	566	2036	9.379e-20
GO:BP	GO:0019222	regulation of metabolic process	1624	7035	1.083e-18
GO:BP	GO:0033044	regulation of chromosome organization	111	242	1.440e-18
GO:BP	GO:0000226	microtubule cytoskeleton organization	231	670	2.119e-18
GO:BP	GO:0060255	regulation of macromolecule metabolic process	1510	6492	3.485e-18
GO:BP	GO:0000070	mitotic sister chromatid segregation	94	193	7.917e-18
GO:BP	GO:0009057	macromolecule catabolic process	413	1417	1.132e-17
GO:BP	GO:0006366	transcription by RNA polymerase II	705	2711	3.933e-17
GO:BP	GO:0007059	chromosome segregation	161	427	1.209e-16
GO:BP	GO:0006302	double-strand break repair	130	319	1.767e-16
GO:BP	GO:0140694	membraneless organelle assembly	161	430	2.556e-16
GO:BP	GO:0051254	positive regulation of RNA metabolic process	503	1835	4.817e-16
GO:BP	GO:0044238	primary metabolic process	2643	12342	5.402e-16
GO:BP	GO:0098813	nuclear chromosome segregation	130	323	5.667e-16
GO:BP	GO:0007346	regulation of mitotic cell cycle	175	492	3.036e-15
GO:BP	GO:0048285	organelle fission	177	500	3.356e-15
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	665	2578	3.489e-15
GO:BP	GO:0071840	cellular component organization or biogenesis	1869	8393	4.898e-15
GO:BP	GO:0051301	cell division	217	658	8.236e-15
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	213	643	9.039e-15
GO:BP	GO:0008033	tRNA processing	71	139	9.039e-15
GO:BP	GO:0007017	microtubule-based process	301	999	1.189e-14
GO:BP	GO:0035556	intracellular signal transduction	746	2965	1.408e-14
GO:BP	GO:0015031	protein transport	406	1444	1.431e-14
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	248	786	1.857e-14
GO:BP	GO:0009894	regulation of catabolic process	310	1040	1.945e-14
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	208	628	1.981e-14
GO:BP	GO:0019941	modification-dependent protein catabolic process	210	638	2.966e-14
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	462	1699	5.133e-14
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	461	1697	6.597e-14
GO:BP	GO:0010498	proteasomal protein catabolic process	184	543	9.242e-14
GO:BP	GO:0000280	nuclear division	160	452	9.522e-14
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	79	169	9.742e-14
GO:BP	GO:0044770	cell cycle phase transition	181	532	9.919e-14
GO:BP	GO:0044772	mitotic cell cycle phase transition	153	428	1.505e-13
GO:BP	GO:0010948	negative regulation of cell cycle process	114	289	2.705e-13
GO:BP	GO:1901987	regulation of cell cycle phase transition	152	427	2.761e-13
GO:BP	GO:0006914	autophagy	196	597	3.558e-13
GO:BP	GO:0061919	process utilizing autophagic mechanism	196	597	3.558e-13
GO:BP	GO:0009987	cellular process	4016	20247	3.952e-13
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	148	414	4.105e-13
GO:BP	GO:0009451	RNA modification	79	174	6.642e-13
GO:BP	GO:0030163	protein catabolic process	301	1030	7.821e-13
GO:BP	GO:0016072	rRNA metabolic process	106	266	1.061e-12
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	123	327	1.262e-12
GO:BP	GO:0071705	nitrogen compound transport	505	1923	1.364e-12
GO:BP	GO:0007005	mitochondrion organization	152	435	1.489e-12
GO:BP	GO:0051052	regulation of DNA metabolic process	169	500	1.521e-12
GO:BP	GO:0007051	spindle organization	88	206	1.580e-12
GO:BP	GO:0010639	negative regulation of organelle organization	129	352	2.667e-12
GO:BP	GO:0000075	cell cycle checkpoint signaling	81	185	3.326e-12
GO:BP	GO:0043687	post-translational protein modification	297	1027	4.604e-12
GO:BP	GO:0042254	ribosome biogenesis	120	323	6.808e-12
GO:BP	GO:0051246	regulation of protein metabolic process	485	1855	1.017e-11
GO:BP	GO:0006400	tRNA modification	51	95	1.096e-11
GO:BP	GO:0007052	mitotic spindle organization	64	134	1.183e-11
GO:BP	GO:0051640	organelle localization	196	620	1.812e-11
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	64	136	2.743e-11
GO:BP	GO:0006796	phosphate-containing compound metabolic process	604	2407	2.826e-11
GO:BP	GO:0006793	phosphorus metabolic process	604	2410	3.587e-11
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	643	2593	4.638e-11
GO:BP	GO:0009896	positive regulation of catabolic process	176	546	4.638e-11
GO:BP	GO:0016043	cellular component organization	1792	8184	5.521e-11
GO:BP	GO:0010638	positive regulation of organelle organization	162	492	5.521e-11
GO:BP	GO:0032446	protein modification by small protein conjugation	251	853	5.521e-11
GO:BP	GO:0045786	negative regulation of cell cycle	132	377	5.757e-11
GO:BP	GO:0061024	membrane organization	243	821	6.555e-11
GO:BP	GO:0044087	regulation of cellular component biogenesis	288	1011	6.989e-11
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	279	975	9.220e-11
GO:BP	GO:0051234	establishment of localization	1132	4928	9.845e-11
GO:BP	GO:0006810	transport	1024	4407	1.044e-10
GO:BP	GO:0030029	actin filament-based process	243	825	1.102e-10
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	96	248	1.120e-10
GO:BP	GO:0045184	establishment of protein localization	497	1937	1.136e-10
GO:BP	GO:0051493	regulation of cytoskeleton organization	167	517	1.355e-10
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	89	225	1.751e-10
GO:BP	GO:0080135	regulation of cellular response to stress	167	519	1.908e-10
GO:BP	GO:0009891	positive regulation of biosynthetic process	660	2696	2.582e-10
GO:BP	GO:0000725	recombinational repair	79	193	3.787e-10
GO:BP	GO:0043484	regulation of RNA splicing	77	187	4.898e-10
GO:BP	GO:0032259	methylation	91	236	5.168e-10
GO:BP	GO:2001251	negative regulation of chromosome organization	49	97	5.179e-10
GO:BP	GO:0000724	double-strand break repair via homologous recombination	77	188	6.573e-10
GO:BP	GO:0051983	regulation of chromosome segregation	60	132	7.581e-10
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	72	172	8.942e-10
GO:BP	GO:0007507	heart development	186	605	9.038e-10
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	62	139	9.179e-10
GO:BP	GO:0022411	cellular component disassembly	146	446	1.038e-09
GO:BP	GO:0051129	negative regulation of cellular component organization	209	701	1.125e-09
GO:BP	GO:0006282	regulation of DNA repair	87	225	1.163e-09
GO:BP	GO:0006364	rRNA processing	87	225	1.163e-09
GO:BP	GO:0043414	macromolecule methylation	58	127	1.241e-09
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	47	93	1.244e-09
GO:BP	GO:0016236	macroautophagy	124	362	1.244e-09
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1268	5644	1.452e-09
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	48	97	1.975e-09
GO:BP	GO:1903311	regulation of mRNA metabolic process	110	312	2.318e-09
GO:BP	GO:0006310	DNA recombination	119	347	2.833e-09
GO:BP	GO:0016073	snRNA metabolic process	34	58	3.758e-09
GO:BP	GO:0006325	chromatin organization	250	884	4.247e-09
GO:BP	GO:0009889	regulation of biosynthetic process	1297	5809	4.425e-09
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	47	96	4.887e-09
GO:BP	GO:0048193	Golgi vesicle transport	109	312	5.122e-09
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	48	100	7.326e-09
GO:BP	GO:0010468	regulation of gene expression	1239	5536	8.159e-09
GO:BP	GO:0006753	nucleoside phosphate metabolic process	192	646	9.148e-09
GO:BP	GO:0044839	cell cycle G2/M phase transition	65	156	9.574e-09
GO:BP	GO:0033045	regulation of sister chromatid segregation	50	107	9.829e-09
GO:BP	GO:0016567	protein ubiquitination	221	768	9.829e-09
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	198	673	1.191e-08
GO:BP	GO:0006886	intracellular protein transport	201	686	1.265e-08
GO:BP	GO:0000723	telomere maintenance	67	164	1.356e-08
GO:BP	GO:0007088	regulation of mitotic nuclear division	54	121	1.555e-08
GO:BP	GO:0051054	positive regulation of DNA metabolic process	102	291	1.555e-08
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	164	535	1.577e-08
GO:BP	GO:1901135	carbohydrate derivative metabolic process	270	983	1.752e-08
GO:BP	GO:0006403	RNA localization	77	200	1.793e-08
GO:BP	GO:0032204	regulation of telomere maintenance	51	112	1.951e-08
GO:BP	GO:0016197	endosomal transport	101	290	2.769e-08
GO:BP	GO:0055007	cardiac muscle cell differentiation	52	117	3.821e-08
GO:BP	GO:1902531	regulation of intracellular signal transduction	484	1953	4.271e-08
GO:BP	GO:0009117	nucleotide metabolic process	152	493	4.374e-08
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	178	600	4.568e-08
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	48	105	5.266e-08
GO:BP	GO:0051656	establishment of organelle localization	151	491	5.948e-08
GO:BP	GO:0007163	establishment or maintenance of cell polarity	85	234	6.166e-08
GO:BP	GO:0048738	cardiac muscle tissue development	85	234	6.166e-08
GO:BP	GO:0032984	protein-containing complex disassembly	91	257	7.270e-08
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	36	69	7.377e-08
GO:BP	GO:0009966	regulation of signal transduction	713	3034	7.584e-08
GO:BP	GO:0086001	cardiac muscle cell action potential	40	81	7.584e-08
GO:BP	GO:0007006	mitochondrial membrane organization	51	116	8.266e-08
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	31	55	8.301e-08
GO:BP	GO:0051310	metaphase chromosome alignment	47	104	1.186e-07
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	54	127	1.189e-07
GO:BP	GO:0010646	regulation of cell communication	806	3486	1.201e-07
GO:BP	GO:0009259	ribonucleotide metabolic process	120	372	1.341e-07
GO:BP	GO:0030031	cell projection assembly	179	613	1.428e-07
GO:BP	GO:0042176	regulation of protein catabolic process	119	369	1.573e-07
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	32	59	1.609e-07
GO:BP	GO:0016180	snRNA processing	23	35	1.662e-07
GO:BP	GO:2001252	positive regulation of chromosome organization	47	105	1.662e-07
GO:BP	GO:0023051	regulation of signaling	803	3478	1.662e-07
GO:BP	GO:0016192	vesicle-mediated transport	401	1592	1.674e-07
GO:BP	GO:0033365	protein localization to organelle	316	1209	1.676e-07
GO:BP	GO:0006289	nucleotide-excision repair	40	83	1.738e-07
GO:BP	GO:0055013	cardiac muscle cell development	39	80	1.788e-07
GO:BP	GO:0051783	regulation of nuclear division	60	149	1.837e-07
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	36	71	1.837e-07
GO:BP	GO:0044782	cilium organization	134	431	2.122e-07
GO:BP	GO:0060271	cilium assembly	127	403	2.158e-07
GO:BP	GO:0051225	spindle assembly	56	136	2.282e-07
GO:BP	GO:0007264	small GTPase-mediated signal transduction	152	505	2.322e-07
GO:BP	GO:2000779	regulation of double-strand break repair	58	143	2.364e-07
GO:BP	GO:0050000	chromosome localization	53	126	2.377e-07
GO:BP	GO:0006417	regulation of translation	121	380	2.473e-07
GO:BP	GO:0019637	organophosphate metabolic process	285	1077	2.708e-07
GO:BP	GO:0030036	actin cytoskeleton organization	205	729	2.784e-07
GO:BP	GO:0051130	positive regulation of cellular component organization	291	1105	3.064e-07
GO:BP	GO:0032790	ribosome disassembly	25	41	3.064e-07
GO:BP	GO:0035051	cardiocyte differentiation	60	151	3.154e-07
GO:BP	GO:0050684	regulation of mRNA processing	55	134	3.411e-07
GO:BP	GO:0051303	establishment of chromosome localization	50	118	4.610e-07
GO:BP	GO:0019693	ribose phosphate metabolic process	120	380	4.710e-07
GO:BP	GO:1990778	protein localization to cell periphery	116	365	5.523e-07
GO:BP	GO:0055006	cardiac cell development	40	86	5.700e-07
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	63	164	6.113e-07
GO:BP	GO:0010256	endomembrane system organization	176	613	6.478e-07
GO:BP	GO:1905818	regulation of chromosome separation	37	77	6.611e-07
GO:BP	GO:1903008	organelle disassembly	35	71	6.994e-07
GO:BP	GO:0031570	DNA integrity checkpoint signaling	51	123	7.618e-07
GO:BP	GO:0045739	positive regulation of DNA repair	55	137	8.248e-07
GO:BP	GO:0032970	regulation of actin filament-based process	118	376	8.853e-07
GO:BP	GO:0051304	chromosome separation	39	84	8.871e-07
GO:BP	GO:0009303	rRNA transcription	24	40	9.021e-07
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	382	1529	9.523e-07
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	82	236	9.767e-07
GO:BP	GO:0030010	establishment of cell polarity	61	159	1.040e-06
GO:BP	GO:0051247	positive regulation of protein metabolic process	273	1039	1.059e-06
GO:BP	GO:0006163	purine nucleotide metabolic process	131	430	1.067e-06
GO:BP	GO:0000077	DNA damage checkpoint signaling	48	114	1.067e-06
GO:BP	GO:0060341	regulation of cellular localization	267	1013	1.107e-06
GO:BP	GO:0072521	purine-containing compound metabolic process	163	563	1.122e-06
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	49	118	1.288e-06
GO:BP	GO:0009150	purine ribonucleotide metabolic process	111	351	1.394e-06
GO:BP	GO:0006402	mRNA catabolic process	88	261	1.458e-06
GO:BP	GO:0007399	nervous system development	611	2604	1.501e-06
GO:BP	GO:0090307	mitotic spindle assembly	36	76	1.515e-06
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	71	197	1.515e-06
GO:BP	GO:0043038	amino acid activation	26	47	2.243e-06
GO:BP	GO:0042770	signal transduction in response to DNA damage	64	173	2.269e-06
GO:BP	GO:0015931	nucleobase-containing compound transport	81	237	2.535e-06
GO:BP	GO:0051784	negative regulation of nuclear division	32	65	2.700e-06
GO:BP	GO:0051306	mitotic sister chromatid separation	32	65	2.700e-06
GO:BP	GO:0030030	cell projection organization	401	1631	2.702e-06
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	31	62	2.717e-06
GO:BP	GO:0051236	establishment of RNA localization	61	163	2.778e-06
GO:BP	GO:0031503	protein-containing complex localization	75	215	2.915e-06
GO:BP	GO:0086003	cardiac muscle cell contraction	37	81	3.098e-06
GO:BP	GO:0072344	rescue of stalled ribosome	21	34	3.098e-06
GO:BP	GO:0061337	cardiac conduction	41	94	3.100e-06
GO:BP	GO:0060048	cardiac muscle contraction	55	142	3.105e-06
GO:BP	GO:0055002	striated muscle cell development	63	171	3.263e-06
GO:BP	GO:0007030	Golgi organization	58	153	3.342e-06
GO:BP	GO:0031032	actomyosin structure organization	74	212	3.355e-06
GO:BP	GO:0007007	inner mitochondrial membrane organization	25	45	3.388e-06
GO:BP	GO:0051053	negative regulation of DNA metabolic process	54	139	3.542e-06
GO:BP	GO:0003007	heart morphogenesis	88	266	3.554e-06
GO:BP	GO:0048583	regulation of response to stimulus	896	3993	3.742e-06
GO:BP	GO:0007275	multicellular organism development	1046	4727	3.826e-06
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	28	54	4.078e-06
GO:BP	GO:0055001	muscle cell development	70	198	4.101e-06
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	46	112	4.454e-06
GO:BP	GO:0044281	small molecule metabolic process	430	1776	5.388e-06
GO:BP	GO:0003015	heart process	84	253	5.646e-06
GO:BP	GO:0032879	regulation of localization	484	2029	5.717e-06
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	167	594	5.731e-06
GO:BP	GO:0043039	tRNA aminoacylation	25	46	5.775e-06
GO:BP	GO:0010212	response to ionizing radiation	54	141	5.886e-06
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	62	170	5.889e-06
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	389	1588	5.971e-06
GO:BP	GO:0006354	DNA-templated transcription elongation	52	134	5.998e-06
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	26	49	6.031e-06
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	26	49	6.031e-06
GO:BP	GO:0071173	spindle assembly checkpoint signaling	26	49	6.031e-06
GO:BP	GO:0000959	mitochondrial RNA metabolic process	27	52	6.269e-06
GO:BP	GO:0006839	mitochondrial transport	64	178	6.645e-06
GO:BP	GO:0006338	chromatin remodeling	197	725	6.645e-06
GO:BP	GO:0032886	regulation of microtubule-based process	87	266	6.861e-06
GO:BP	GO:0048523	negative regulation of cellular process	1225	5629	7.694e-06
GO:BP	GO:0014706	striated muscle tissue development	122	408	8.089e-06
GO:BP	GO:0045732	positive regulation of protein catabolic process	72	209	8.121e-06
GO:BP	GO:0060047	heart contraction	81	244	8.813e-06
GO:BP	GO:0042692	muscle cell differentiation	121	405	9.417e-06
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	85	260	9.436e-06
GO:BP	GO:0001510	RNA methylation	36	81	9.436e-06
GO:BP	GO:0060537	muscle tissue development	127	430	9.556e-06
GO:BP	GO:0032200	telomere organization	67	191	9.663e-06
GO:BP	GO:0031577	spindle checkpoint signaling	26	50	9.738e-06
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	89	276	9.747e-06
GO:BP	GO:0086065	cell communication involved in cardiac conduction	28	56	9.875e-06
GO:BP	GO:0032880	regulation of protein localization	237	907	1.147e-05
GO:BP	GO:1902115	regulation of organelle assembly	78	234	1.169e-05
GO:BP	GO:0051146	striated muscle cell differentiation	95	301	1.177e-05
GO:BP	GO:0061061	muscle structure development	188	693	1.337e-05
GO:BP	GO:0034976	response to endoplasmic reticulum stress	87	270	1.337e-05
GO:BP	GO:0008016	regulation of heart contraction	70	204	1.337e-05
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	30	63	1.430e-05
GO:BP	GO:0031399	regulation of protein modification process	268	1049	1.499e-05
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	28	57	1.530e-05
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	45	113	1.530e-05
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	26	51	1.533e-05
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	26	51	1.533e-05
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	26	51	1.533e-05
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	26	51	1.533e-05
GO:BP	GO:0031109	microtubule polymerization or depolymerization	52	138	1.579e-05
GO:BP	GO:0050658	RNA transport	58	160	1.616e-05
GO:BP	GO:0050657	nucleic acid transport	58	160	1.616e-05
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	33	73	1.686e-05
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	36	83	1.812e-05
GO:BP	GO:0000209	protein polyubiquitination	89	280	1.836e-05
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	21	37	1.867e-05
GO:BP	GO:0035966	response to topologically incorrect protein	57	157	1.876e-05
GO:BP	GO:0032502	developmental process	1405	6553	1.928e-05
GO:BP	GO:0048856	anatomical structure development	1293	5997	2.212e-05
GO:BP	GO:0008152	metabolic process	2879	14136	2.212e-05
GO:BP	GO:0006418	tRNA aminoacylation for protein translation	23	43	2.242e-05
GO:BP	GO:1902903	regulation of supramolecular fiber organization	114	383	2.268e-05
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	28	58	2.270e-05
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	51	136	2.292e-05
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	51	136	2.292e-05
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	33	74	2.375e-05
GO:BP	GO:0010506	regulation of autophagy	110	367	2.397e-05
GO:BP	GO:0006986	response to unfolded protein	52	140	2.501e-05
GO:BP	GO:0006360	transcription by RNA polymerase I	32	71	2.580e-05
GO:BP	GO:0065009	regulation of molecular function	364	1496	2.611e-05
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	95	307	2.842e-05
GO:BP	GO:0072659	protein localization to plasma membrane	91	291	2.888e-05
GO:BP	GO:0006915	apoptotic process	455	1923	3.029e-05
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	49	130	3.066e-05
GO:BP	GO:0006950	response to stress	876	3948	3.267e-05
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	83	260	3.344e-05
GO:BP	GO:0032206	positive regulation of telomere maintenance	33	75	3.344e-05
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	311	1256	3.403e-05
GO:BP	GO:0048731	system development	897	4053	3.569e-05
GO:BP	GO:1905819	negative regulation of chromosome separation	26	53	3.606e-05
GO:BP	GO:0051985	negative regulation of chromosome segregation	26	53	3.606e-05
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	26	53	3.606e-05
GO:BP	GO:0051294	establishment of spindle orientation	24	47	3.663e-05
GO:BP	GO:0051169	nuclear transport	101	334	4.072e-05
GO:BP	GO:0006913	nucleocytoplasmic transport	101	334	4.072e-05
GO:BP	GO:0072359	circulatory system development	286	1145	4.245e-05
GO:BP	GO:0031123	RNA 3’-end processing	39	96	4.257e-05
GO:BP	GO:0045787	positive regulation of cell cycle	105	351	4.393e-05
GO:BP	GO:0141188	nucleic acid catabolic process	103	343	4.530e-05
GO:BP	GO:0090068	positive regulation of cell cycle process	83	262	4.547e-05
GO:BP	GO:0044093	positive regulation of molecular function	228	884	4.566e-05
GO:BP	GO:0051716	cellular response to stimulus	1563	7376	4.907e-05
GO:BP	GO:0006401	RNA catabolic process	96	315	4.941e-05
GO:BP	GO:0006260	DNA replication	88	283	5.271e-05
GO:BP	GO:0086026	atrial cardiac muscle cell to AV node cell signaling	13	18	5.306e-05
GO:BP	GO:0086014	atrial cardiac muscle cell action potential	13	18	5.306e-05
GO:BP	GO:0070979	protein K11-linked ubiquitination	21	39	5.306e-05
GO:BP	GO:0086066	atrial cardiac muscle cell to AV node cell communication	13	18	5.306e-05
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	31	70	5.557e-05
GO:BP	GO:0006941	striated muscle contraction	64	189	5.766e-05
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	80	253	7.316e-05
GO:BP	GO:0086004	regulation of cardiac muscle cell contraction	19	34	7.773e-05
GO:BP	GO:0022604	regulation of cell morphogenesis	78	246	8.599e-05
GO:BP	GO:0034330	cell junction organization	215	834	9.060e-05
GO:BP	GO:0048519	negative regulation of biological process	1252	5834	9.076e-05
GO:BP	GO:1901800	positive regulation of proteasomal protein catabolic process	43	113	9.423e-05
GO:BP	GO:0012501	programmed cell death	464	1987	9.770e-05
GO:BP	GO:0051168	nuclear export	58	169	1.038e-04
GO:BP	GO:0044380	protein localization to cytoskeleton	28	62	1.049e-04
GO:BP	GO:0006383	transcription by RNA polymerase III	28	62	1.049e-04
GO:BP	GO:0018193	peptidyl-amino acid modification	181	686	1.194e-04
GO:BP	GO:0008219	cell death	464	1991	1.208e-04
GO:BP	GO:0086019	cell-cell signaling involved in cardiac conduction	18	32	1.220e-04
GO:BP	GO:0042790	nucleolar large rRNA transcription by RNA polymerase I	15	24	1.295e-04
GO:BP	GO:2000781	positive regulation of double-strand break repair	37	93	1.303e-04
GO:BP	GO:0097435	supramolecular fiber organization	220	861	1.303e-04
GO:BP	GO:0000460	maturation of 5.8S rRNA	19	35	1.330e-04
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	19	35	1.330e-04
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	51	144	1.373e-04
GO:BP	GO:0000018	regulation of DNA recombination	51	144	1.373e-04
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	23	47	1.398e-04
GO:BP	GO:0000966	RNA 5’-end processing	20	38	1.398e-04
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	45	122	1.423e-04
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	175	662	1.466e-04
GO:BP	GO:0016482	cytosolic transport	50	141	1.604e-04
GO:BP	GO:0051028	mRNA transport	47	130	1.656e-04
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	30	70	1.699e-04
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	45	123	1.801e-04
GO:BP	GO:0031023	microtubule organizing center organization	53	153	1.858e-04
GO:BP	GO:0000910	cytokinesis	63	192	2.045e-04
GO:BP	GO:0035967	cellular response to topologically incorrect protein	41	109	2.062e-04
GO:BP	GO:0048284	organelle fusion	56	165	2.077e-04
GO:BP	GO:0090148	membrane fission	22	45	2.218e-04
GO:BP	GO:0000281	mitotic cytokinesis	37	95	2.219e-04
GO:BP	GO:0032205	negative regulation of telomere maintenance	20	39	2.255e-04
GO:BP	GO:0099622	cardiac muscle cell membrane repolarization	20	39	2.255e-04
GO:BP	GO:0090407	organophosphate biosynthetic process	164	619	2.421e-04
GO:BP	GO:1901836	regulation of transcription of nucleolar large rRNA by RNA polymerase I	11	15	2.477e-04
GO:BP	GO:0086064	cell communication by electrical coupling involved in cardiac conduction	15	25	2.484e-04
GO:BP	GO:0046034	ATP metabolic process	72	229	2.547e-04
GO:BP	GO:1905515	non-motile cilium assembly	29	68	2.608e-04
GO:BP	GO:0051653	spindle localization	29	68	2.608e-04
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	25	55	2.741e-04
GO:BP	GO:0055117	regulation of cardiac muscle contraction	31	75	2.810e-04
GO:BP	GO:0018205	peptidyl-lysine modification	49	140	2.824e-04
GO:BP	GO:0007098	centrosome cycle	49	140	2.824e-04
GO:BP	GO:0006352	DNA-templated transcription initiation	67	210	2.941e-04
GO:BP	GO:0070252	actin-mediated cell contraction	41	111	3.304e-04
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	32	79	3.320e-04
GO:BP	GO:0141124	intracellular signaling cassette	443	1912	3.411e-04
GO:BP	GO:0006261	DNA-templated DNA replication	54	160	3.421e-04
GO:BP	GO:0040001	establishment of mitotic spindle localization	21	43	3.429e-04
GO:BP	GO:0062125	regulation of mitochondrial gene expression	18	34	3.429e-04
GO:BP	GO:0140058	neuron projection arborization	18	34	3.429e-04
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	18	34	3.429e-04
GO:BP	GO:0016050	vesicle organization	107	376	3.466e-04
GO:BP	GO:0006626	protein targeting to mitochondrion	39	104	3.466e-04
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	26	59	3.493e-04
GO:BP	GO:0000132	establishment of mitotic spindle orientation	19	37	3.493e-04
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	97	334	3.493e-04
GO:BP	GO:0086002	cardiac muscle cell action potential involved in contraction	26	59	3.493e-04
GO:BP	GO:0051865	protein autoubiquitination	31	76	3.699e-04
GO:BP	GO:0046602	regulation of mitotic centrosome separation	8	9	3.793e-04
GO:BP	GO:0031647	regulation of protein stability	97	335	3.948e-04
GO:BP	GO:0034620	cellular response to unfolded protein	36	94	4.193e-04
GO:BP	GO:0086009	membrane repolarization	24	53	4.193e-04
GO:BP	GO:0006414	translational elongation	32	80	4.315e-04
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	39	105	4.365e-04
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	27	63	4.371e-04
GO:BP	GO:0051293	establishment of spindle localization	27	63	4.371e-04
GO:BP	GO:0097352	autophagosome maturation	27	63	4.371e-04
GO:BP	GO:1903322	positive regulation of protein modification by small protein conjugation or removal	46	131	4.414e-04
GO:BP	GO:0099643	signal release from synapse	51	150	4.414e-04
GO:BP	GO:0007269	neurotransmitter secretion	51	150	4.414e-04
GO:BP	GO:1901292	nucleoside phosphate catabolic process	60	185	4.436e-04
GO:BP	GO:0050790	regulation of catalytic activity	231	928	4.483e-04
GO:BP	GO:0051253	negative regulation of RNA metabolic process	333	1400	4.648e-04
GO:BP	GO:0036503	ERAD pathway	40	109	4.655e-04
GO:BP	GO:0009166	nucleotide catabolic process	54	162	4.770e-04
GO:BP	GO:0007004	telomere maintenance via telomerase	26	60	4.808e-04
GO:BP	GO:0060236	regulation of mitotic spindle organization	21	44	5.040e-04
GO:BP	GO:0016358	dendrite development	74	242	5.109e-04
GO:BP	GO:0006139	nucleobase-containing compound metabolic process	1669	7992	5.164e-04
GO:BP	GO:0071478	cellular response to radiation	59	182	5.164e-04
GO:BP	GO:0006893	Golgi to plasma membrane transport	28	67	5.252e-04
GO:BP	GO:1901875	positive regulation of post-translational protein modification	46	132	5.324e-04
GO:BP	GO:0070585	protein localization to mitochondrion	46	132	5.324e-04
GO:BP	GO:1905508	protein localization to microtubule organizing center	19	38	5.328e-04
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	52	155	5.393e-04
GO:BP	GO:0071806	protein transmembrane transport	30	74	5.452e-04
GO:BP	GO:0051383	kinetochore organization	13	21	5.499e-04
GO:BP	GO:0050808	synapse organization	149	563	5.688e-04
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	37	99	5.707e-04
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	73	239	5.871e-04
GO:BP	GO:0031297	replication fork processing	23	51	6.347e-04
GO:BP	GO:1903522	regulation of blood circulation	77	256	6.435e-04
GO:BP	GO:0043009	chordate embryonic development	173	671	6.435e-04
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	42	118	6.535e-04
GO:BP	GO:1901873	regulation of post-translational protein modification	74	244	6.690e-04
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	14	24	6.720e-04
GO:BP	GO:0006479	protein methylation	22	48	6.807e-04
GO:BP	GO:0008213	protein alkylation	22	48	6.807e-04
GO:BP	GO:0090224	regulation of spindle organization	22	48	6.807e-04
GO:BP	GO:0001508	action potential	56	172	6.860e-04
GO:BP	GO:0009260	ribonucleotide biosynthetic process	57	176	6.930e-04
GO:BP	GO:0016310	phosphorylation	314	1320	7.512e-04
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	33	86	8.040e-04
GO:BP	GO:0003205	cardiac chamber development	55	169	8.074e-04
GO:BP	GO:0010927	cellular component assembly involved in morphogenesis	47	138	8.096e-04
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	47	138	8.096e-04
GO:BP	GO:0071479	cellular response to ionizing radiation	29	72	8.178e-04
GO:BP	GO:0071025	RNA surveillance	12	19	8.201e-04
GO:BP	GO:0043085	positive regulation of catalytic activity	146	554	8.201e-04
GO:BP	GO:0110154	RNA decapping	12	19	8.201e-04
GO:BP	GO:0010644	cell communication by electrical coupling	17	33	8.238e-04
GO:BP	GO:0008053	mitochondrial fusion	17	33	8.238e-04
GO:BP	GO:0009653	anatomical structure morphogenesis	605	2713	8.955e-04
GO:BP	GO:0009314	response to radiation	119	437	9.174e-04
GO:BP	GO:0030239	myofibril assembly	30	76	9.365e-04
GO:BP	GO:0043087	regulation of GTPase activity	63	202	9.675e-04
GO:BP	GO:0003012	muscle system process	119	438	1.015e-03
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	43	124	1.026e-03
GO:BP	GO:0006390	mitochondrial transcription	13	22	1.030e-03
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	36	98	1.045e-03
GO:BP	GO:0043254	regulation of protein-containing complex assembly	115	421	1.045e-03
GO:BP	GO:0031122	cytoplasmic microtubule organization	27	66	1.052e-03
GO:BP	GO:0009895	negative regulation of catabolic process	101	361	1.069e-03
GO:BP	GO:0051648	vesicle localization	67	219	1.085e-03
GO:BP	GO:0007015	actin filament organization	124	461	1.137e-03
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	176	692	1.146e-03
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	134	505	1.151e-03
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	26	63	1.192e-03
GO:BP	GO:1903115	regulation of actin filament-based movement	19	40	1.199e-03
GO:BP	GO:0030488	tRNA methylation	19	40	1.199e-03
GO:BP	GO:0002098	tRNA wobble uridine modification	11	17	1.219e-03
GO:BP	GO:1905037	autophagosome organization	43	125	1.236e-03
GO:BP	GO:0099003	vesicle-mediated transport in synapse	76	257	1.243e-03
GO:BP	GO:0071539	protein localization to centrosome	18	37	1.250e-03
GO:BP	GO:0098901	regulation of cardiac muscle cell action potential	15	28	1.250e-03
GO:BP	GO:0086005	ventricular cardiac muscle cell action potential	17	34	1.284e-03
GO:BP	GO:0051650	establishment of vesicle localization	62	200	1.292e-03
GO:BP	GO:0071897	DNA biosynthetic process	55	172	1.294e-03
GO:BP	GO:0065008	regulation of biological quality	651	2947	1.314e-03
GO:BP	GO:1901838	positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	8	10	1.314e-03
GO:BP	GO:0032506	cytokinetic process	22	50	1.349e-03
GO:BP	GO:0000045	autophagosome assembly	41	118	1.376e-03
GO:BP	GO:0048813	dendrite morphogenesis	48	145	1.408e-03
GO:BP	GO:1904375	regulation of protein localization to cell periphery	49	149	1.433e-03
GO:BP	GO:0034475	U4 snRNA 3’-end processing	7	8	1.440e-03
GO:BP	GO:0150012	positive regulation of neuron projection arborization	7	8	1.440e-03
GO:BP	GO:0006984	ER-nucleus signaling pathway	21	47	1.479e-03
GO:BP	GO:0051668	localization within membrane	226	924	1.526e-03
GO:BP	GO:0002097	tRNA wobble base modification	12	20	1.556e-03
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	89	314	1.665e-03
GO:BP	GO:0009201	ribonucleoside triphosphate biosynthetic process	41	119	1.679e-03
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	58	186	1.767e-03
GO:BP	GO:0055012	ventricular cardiac muscle cell differentiation	10	15	1.767e-03
GO:BP	GO:0071027	nuclear RNA surveillance	10	15	1.767e-03
GO:BP	GO:0010970	transport along microtubule	56	178	1.767e-03
GO:BP	GO:0001325	formation of extrachromosomal circular DNA	10	15	1.767e-03
GO:BP	GO:0150011	regulation of neuron projection arborization	10	15	1.767e-03
GO:BP	GO:0090656	t-circle formation	10	15	1.767e-03
GO:BP	GO:0090737	telomere maintenance via telomere trimming	10	15	1.767e-03
GO:BP	GO:0009790	embryo development	271	1135	1.772e-03
GO:BP	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	18	38	1.845e-03
GO:BP	GO:0045214	sarcomere organization	22	51	1.860e-03
GO:BP	GO:0043547	positive regulation of GTPase activity	45	135	1.870e-03
GO:BP	GO:0000154	rRNA modification	17	35	1.936e-03
GO:BP	GO:0002027	regulation of heart rate	36	101	1.972e-03
GO:BP	GO:0099625	ventricular cardiac muscle cell membrane repolarization	15	29	1.998e-03
GO:BP	GO:0046390	ribose phosphate biosynthetic process	57	183	2.042e-03
GO:BP	GO:0006513	protein monoubiquitination	21	48	2.060e-03
GO:BP	GO:1901976	regulation of cell cycle checkpoint	21	48	2.060e-03
GO:BP	GO:0006508	proteolysis	345	1486	2.110e-03
GO:BP	GO:0030048	actin filament-based movement	45	136	2.240e-03
GO:BP	GO:0006220	pyrimidine nucleotide metabolic process	23	55	2.271e-03
GO:BP	GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	11	18	2.378e-03
GO:BP	GO:0017004	cytochrome complex assembly	19	42	2.508e-03
GO:BP	GO:0099173	postsynapse organization	72	246	2.512e-03
GO:BP	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	30	80	2.519e-03
GO:BP	GO:0001682	tRNA 5’-leader removal	9	13	2.561e-03
GO:BP	GO:0051258	protein polymerization	81	284	2.568e-03
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	63	209	2.573e-03
GO:BP	GO:0110053	regulation of actin filament organization	76	263	2.580e-03
GO:BP	GO:0043487	regulation of RNA stability	59	193	2.692e-03
GO:BP	GO:1905475	regulation of protein localization to membrane	59	193	2.692e-03
GO:BP	GO:0007031	peroxisome organization	18	39	2.692e-03
GO:BP	GO:0043488	regulation of mRNA stability	56	181	2.759e-03
GO:BP	GO:0086012	membrane depolarization during cardiac muscle cell action potential	12	21	2.789e-03
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	36	103	2.990e-03
GO:BP	GO:0061842	microtubule organizing center localization	16	33	3.035e-03
GO:BP	GO:0051642	centrosome localization	16	33	3.035e-03
GO:BP	GO:0009218	pyrimidine ribonucleotide metabolic process	16	33	3.035e-03
GO:BP	GO:1990928	response to amino acid starvation	23	56	3.046e-03
GO:BP	GO:0061013	regulation of mRNA catabolic process	60	198	3.058e-03
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	37	107	3.100e-03
GO:BP	GO:0008535	respiratory chain complex IV assembly	15	30	3.113e-03
GO:BP	GO:0051984	positive regulation of chromosome segregation	15	30	3.113e-03
GO:BP	GO:0006284	base-excision repair	20	46	3.164e-03
GO:BP	GO:0080134	regulation of response to stress	322	1387	3.430e-03
GO:BP	GO:0030490	maturation of SSU-rRNA	22	53	3.453e-03
GO:BP	GO:0034394	protein localization to cell surface	26	67	3.504e-03
GO:BP	GO:1905168	positive regulation of double-strand break repair via homologous recombination	19	43	3.513e-03
GO:BP	GO:0071028	nuclear mRNA surveillance	8	11	3.553e-03
GO:BP	GO:0030953	astral microtubule organization	8	11	3.553e-03
GO:BP	GO:0099116	tRNA 5’-end processing	10	16	3.576e-03
GO:BP	GO:0016074	sno(s)RNA metabolic process	10	16	3.576e-03
GO:BP	GO:0046036	CTP metabolic process	10	16	3.576e-03
GO:BP	GO:0009967	positive regulation of signal transduction	362	1578	3.583e-03
GO:BP	GO:0035418	protein localization to synapse	32	89	3.614e-03
GO:BP	GO:0032386	regulation of intracellular transport	76	266	3.629e-03
GO:BP	GO:0003279	cardiac septum development	37	108	3.727e-03
GO:BP	GO:0031398	positive regulation of protein ubiquitination	37	108	3.727e-03
GO:BP	GO:0031929	TOR signaling	52	167	3.737e-03
GO:BP	GO:0001701	in utero embryonic development	110	413	3.744e-03
GO:BP	GO:0071214	cellular response to abiotic stimulus	93	339	3.744e-03
GO:BP	GO:0104004	cellular response to environmental stimulus	93	339	3.744e-03
GO:BP	GO:0006942	regulation of striated muscle contraction	34	97	4.015e-03
GO:BP	GO:0006275	regulation of DNA replication	40	120	4.048e-03
GO:BP	GO:0099504	synaptic vesicle cycle	65	221	4.143e-03
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	28	75	4.222e-03
GO:BP	GO:0060039	pericardium development	11	19	4.290e-03
GO:BP	GO:0006936	muscle contraction	95	349	4.297e-03
GO:BP	GO:0035567	non-canonical Wnt signaling pathway	26	68	4.456e-03
GO:BP	GO:0097120	receptor localization to synapse	29	79	4.581e-03
GO:BP	GO:0031396	regulation of protein ubiquitination	59	197	4.615e-03
GO:BP	GO:0043622	cortical microtubule organization	7	9	4.650e-03
GO:BP	GO:0000467	exonucleolytic trimming to generate mature 3’-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	7	9	4.650e-03
GO:BP	GO:0003162	atrioventricular node development	7	9	4.650e-03
GO:BP	GO:0006304	DNA modification	15	31	4.671e-03
GO:BP	GO:0032465	regulation of cytokinesis	33	94	4.671e-03
GO:BP	GO:0034472	snRNA 3’-end processing	12	22	4.680e-03
GO:BP	GO:0086013	membrane repolarization during cardiac muscle cell action potential	13	25	4.857e-03
GO:BP	GO:0046785	microtubule polymerization	34	98	4.867e-03
GO:BP	GO:0003300	cardiac muscle hypertrophy	30	83	4.867e-03
GO:BP	GO:0003292	cardiac septum cell differentiation	5	5	4.897e-03
GO:BP	GO:0060922	atrioventricular node cell differentiation	5	5	4.897e-03
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	43	133	4.985e-03
GO:BP	GO:0009152	purine ribonucleotide biosynthetic process	50	161	5.026e-03
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	301	1296	5.026e-03
GO:BP	GO:0061157	mRNA destabilization	35	102	5.027e-03
GO:BP	GO:0061951	establishment of protein localization to plasma membrane	25	65	5.073e-03
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	31	87	5.129e-03
GO:BP	GO:0050779	RNA destabilization	36	106	5.181e-03
GO:BP	GO:0000902	cell morphogenesis	237	996	5.181e-03
GO:BP	GO:0043144	sno(s)RNA processing	9	14	5.276e-03
GO:BP	GO:0007100	mitotic centrosome separation	9	14	5.276e-03
GO:BP	GO:0031401	positive regulation of protein modification process	159	637	5.382e-03
GO:BP	GO:0071035	nuclear polyadenylation-dependent rRNA catabolic process	6	7	5.422e-03
GO:BP	GO:0071038	TRAMP-dependent tRNA surveillance pathway	6	7	5.422e-03
GO:BP	GO:0040031	snRNA modification	6	7	5.422e-03
GO:BP	GO:0022008	neurogenesis	400	1771	5.749e-03
GO:BP	GO:0098534	centriole assembly	20	48	5.752e-03
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	297	1280	5.752e-03
GO:BP	GO:0070936	protein K48-linked ubiquitination	34	99	5.846e-03
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	201	831	5.865e-03
GO:BP	GO:0046902	regulation of mitochondrial membrane permeability	22	55	5.898e-03
GO:BP	GO:0031346	positive regulation of cell projection organization	96	357	5.975e-03
GO:BP	GO:0038202	TORC1 signaling	35	103	6.025e-03
GO:BP	GO:1903829	positive regulation of protein localization	128	499	6.173e-03
GO:BP	GO:0016239	positive regulation of macroautophagy	31	88	6.271e-03
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	167	676	6.375e-03
GO:BP	GO:0009247	glycolipid biosynthetic process	28	77	6.524e-03
GO:BP	GO:0048858	cell projection morphogenesis	168	681	6.559e-03
GO:BP	GO:0072523	purine-containing compound catabolic process	48	155	6.712e-03
GO:BP	GO:0045333	cellular respiration	69	242	6.712e-03
GO:BP	GO:0051494	negative regulation of cytoskeleton organization	48	155	6.712e-03
GO:BP	GO:0006413	translational initiation	41	127	6.712e-03
GO:BP	GO:0009142	nucleoside triphosphate biosynthetic process	41	127	6.712e-03
GO:BP	GO:0003231	cardiac ventricle development	41	127	6.712e-03
GO:BP	GO:0006091	generation of precursor metabolites and energy	123	478	6.839e-03
GO:BP	GO:0086010	membrane depolarization during action potential	14	29	7.184e-03
GO:BP	GO:0034508	centromere complex assembly	14	29	7.184e-03
GO:BP	GO:0042407	cristae formation	11	20	7.206e-03
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	18	42	7.222e-03
GO:BP	GO:0001570	vasculogenesis	30	85	7.279e-03
GO:BP	GO:0070129	regulation of mitochondrial translation	13	26	7.432e-03
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	12	23	7.457e-03
GO:BP	GO:0050686	negative regulation of mRNA processing	12	23	7.457e-03
GO:BP	GO:1903578	regulation of ATP metabolic process	27	74	7.514e-03
GO:BP	GO:0009628	response to abiotic stimulus	267	1144	7.514e-03
GO:BP	GO:1904779	regulation of protein localization to centrosome	8	12	7.745e-03
GO:BP	GO:0045862	positive regulation of proteolysis	63	218	7.745e-03
GO:BP	GO:0031126	sno(s)RNA 3’-end processing	8	12	7.745e-03
GO:BP	GO:0017148	negative regulation of translation	42	132	7.864e-03
GO:BP	GO:0072657	protein localization to membrane	199	827	7.922e-03
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	17	39	7.988e-03
GO:BP	GO:0045911	positive regulation of DNA recombination	28	78	7.988e-03
GO:BP	GO:0009968	negative regulation of signal transduction	305	1326	8.329e-03
GO:BP	GO:0110020	regulation of actomyosin structure organization	34	101	8.396e-03
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	19	46	8.648e-03
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	26	71	8.753e-03
GO:BP	GO:0034198	cellular response to amino acid starvation	21	53	8.761e-03
GO:BP	GO:0014897	striated muscle hypertrophy	30	86	8.842e-03
GO:BP	GO:0090630	activation of GTPase activity	16	36	8.842e-03
GO:BP	GO:0006301	postreplication repair	16	36	8.842e-03
GO:BP	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	37	113	8.865e-03
GO:BP	GO:0051248	negative regulation of protein metabolic process	166	677	9.046e-03
GO:BP	GO:0030162	regulation of proteolysis	106	406	9.166e-03
GO:BP	GO:0071824	protein-DNA complex organization	73	262	9.215e-03
GO:BP	GO:0070085	glycosylation	69	245	9.282e-03
GO:BP	GO:0061512	protein localization to cilium	27	75	9.282e-03
GO:BP	GO:0019220	regulation of phosphate metabolic process	226	956	9.450e-03
GO:BP	GO:0065004	protein-DNA complex assembly	68	241	9.543e-03
GO:BP	GO:0007099	centriole replication	18	43	9.719e-03
GO:BP	GO:0099111	microtubule-based transport	63	220	9.736e-03
GO:BP	GO:0030865	cortical cytoskeleton organization	22	57	9.787e-03
GO:BP	GO:0048812	neuron projection morphogenesis	162	660	9.814e-03
GO:BP	GO:0106074	aminoacyl-tRNA metabolism involved in translational fidelity	9	15	9.842e-03
GO:BP	GO:0043248	proteasome assembly	9	15	9.842e-03
GO:BP	GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	9	15	9.842e-03
GO:BP	GO:0086069	bundle of His cell to Purkinje myocyte communication	9	15	9.842e-03
GO:BP	GO:0051174	regulation of phosphorus metabolic process	226	957	9.881e-03
GO:BP	GO:0046434	organophosphate catabolic process	69	246	1.029e-02
GO:BP	GO:0009165	nucleotide biosynthetic process	65	229	1.029e-02
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	46	150	1.032e-02
GO:BP	GO:1904357	negative regulation of telomere maintenance via telomere lengthening	14	30	1.035e-02
GO:BP	GO:0009145	purine nucleoside triphosphate biosynthetic process	37	114	1.036e-02
GO:BP	GO:0006195	purine nucleotide catabolic process	43	138	1.051e-02
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	40	126	1.052e-02
GO:BP	GO:0006468	protein phosphorylation	283	1227	1.052e-02
GO:BP	GO:0035050	embryonic heart tube development	30	87	1.058e-02
GO:BP	GO:0140238	presynaptic endocytosis	30	87	1.058e-02
GO:BP	GO:0006405	RNA export from nucleus	31	91	1.096e-02
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	13	27	1.096e-02
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	51	171	1.100e-02
GO:BP	GO:0031125	rRNA 3’-end processing	7	10	1.102e-02
GO:BP	GO:0009220	pyrimidine ribonucleotide biosynthetic process	12	24	1.138e-02
GO:BP	GO:0009147	pyrimidine nucleoside triphosphate metabolic process	12	24	1.138e-02
GO:BP	GO:0031344	regulation of cell projection organization	161	658	1.143e-02
GO:BP	GO:0006450	regulation of translational fidelity	11	21	1.144e-02
GO:BP	GO:0016079	synaptic vesicle exocytosis	33	99	1.149e-02
GO:BP	GO:0150115	cell-substrate junction organization	34	103	1.172e-02
GO:BP	GO:0007033	vacuole organization	67	239	1.203e-02
GO:BP	GO:0003230	cardiac atrium development	16	37	1.205e-02
GO:BP	GO:0060627	regulation of vesicle-mediated transport	133	531	1.205e-02
GO:BP	GO:0010821	regulation of mitochondrion organization	37	115	1.211e-02
GO:BP	GO:0090257	regulation of muscle system process	65	231	1.276e-02
GO:BP	GO:0014896	muscle hypertrophy	30	88	1.280e-02
GO:BP	GO:0008610	lipid biosynthetic process	176	729	1.280e-02
GO:BP	GO:0045910	negative regulation of DNA recombination	20	51	1.280e-02
GO:BP	GO:0072331	signal transduction by p53 class mediator	49	164	1.292e-02
GO:BP	GO:0072522	purine-containing compound biosynthetic process	71	257	1.315e-02
GO:BP	GO:0003143	embryonic heart tube morphogenesis	26	73	1.315e-02
GO:BP	GO:0060914	heart formation	15	34	1.337e-02
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	58	202	1.371e-02
GO:BP	GO:0042274	ribosomal small subunit biogenesis	34	104	1.392e-02
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	91	345	1.422e-02
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	37	116	1.426e-02
GO:BP	GO:0032509	endosome transport via multivesicular body sorting pathway	17	41	1.456e-02
GO:BP	GO:0007064	mitotic sister chromatid cohesion	14	31	1.474e-02
GO:BP	GO:0065002	intracellular protein transmembrane transport	14	31	1.474e-02
GO:BP	GO:0010508	positive regulation of autophagy	48	161	1.502e-02
GO:BP	GO:0090481	pyrimidine nucleotide-sugar transmembrane transport	8	13	1.503e-02
GO:BP	GO:0120180	cell-substrate junction disassembly	6	8	1.534e-02
GO:BP	GO:0120181	focal adhesion disassembly	6	8	1.534e-02
GO:BP	GO:0106354	tRNA surveillance	6	8	1.534e-02
GO:BP	GO:0071051	poly(A)-dependent snoRNA 3’-end processing	6	8	1.534e-02
GO:BP	GO:1904354	negative regulation of telomere capping	6	8	1.534e-02
GO:BP	GO:0030522	intracellular receptor signaling pathway	98	377	1.537e-02
GO:BP	GO:0042325	regulation of phosphorylation	197	830	1.546e-02
GO:BP	GO:2000819	regulation of nucleotide-excision repair	13	28	1.597e-02
GO:BP	GO:0051298	centrosome duplication	26	74	1.613e-02
GO:BP	GO:0006836	neurotransmitter transport	60	212	1.629e-02
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	38	121	1.658e-02
GO:BP	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	38	121	1.658e-02
GO:BP	GO:0032981	mitochondrial respiratory chain complex I assembly	23	63	1.676e-02
GO:BP	GO:0010257	NADH dehydrogenase complex assembly	23	63	1.676e-02
GO:BP	GO:0003229	ventricular cardiac muscle tissue development	23	63	1.676e-02
GO:BP	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	18	45	1.677e-02
GO:BP	GO:1903779	regulation of cardiac conduction	12	25	1.692e-02
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	12	25	1.692e-02
GO:BP	GO:1904292	regulation of ERAD pathway	12	25	1.692e-02
GO:BP	GO:1903241	U2-type prespliceosome assembly	12	25	1.692e-02
GO:BP	GO:0110156	mRNA methylguanosine-cap decapping	9	16	1.694e-02
GO:BP	GO:0051299	centrosome separation	9	16	1.694e-02
GO:BP	GO:0043328	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	9	16	1.694e-02
GO:BP	GO:1990166	protein localization to site of double-strand break	9	16	1.694e-02
GO:BP	GO:0048025	negative regulation of mRNA splicing, via spliceosome	11	22	1.761e-02
GO:BP	GO:0000212	meiotic spindle organization	11	22	1.761e-02
GO:BP	GO:0001947	heart looping	24	67	1.769e-02
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	10	19	1.770e-02
GO:BP	GO:1904505	regulation of telomere maintenance in response to DNA damage	10	19	1.770e-02
GO:BP	GO:0048699	generation of neurons	345	1536	1.781e-02
GO:BP	GO:0032006	regulation of TOR signaling	44	146	1.790e-02
GO:BP	GO:0034644	cellular response to UV	30	90	1.808e-02
GO:BP	GO:0006486	protein glycosylation	63	226	1.827e-02
GO:BP	GO:0043413	macromolecule glycosylation	63	226	1.827e-02
GO:BP	GO:0045727	positive regulation of translation	42	138	1.831e-02
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	42	138	1.831e-02
GO:BP	GO:0106027	neuron projection organization	31	94	1.833e-02
GO:BP	GO:0033120	positive regulation of RNA splicing	19	49	1.865e-02
GO:BP	GO:0042073	intraciliary transport	19	49	1.865e-02
GO:BP	GO:0034502	protein localization to chromosome	39	126	1.878e-02
GO:BP	GO:0003013	circulatory system process	147	602	1.883e-02
GO:BP	GO:0016241	regulation of macroautophagy	53	184	1.914e-02
GO:BP	GO:0051661	maintenance of centrosome location	5	6	1.926e-02
GO:BP	GO:0043954	cellular component maintenance	26	75	1.926e-02
GO:BP	GO:0051096	positive regulation of helicase activity	5	6	1.926e-02
GO:BP	GO:0032471	negative regulation of endoplasmic reticulum calcium ion concentration	5	6	1.926e-02
GO:BP	GO:1990116	ribosome-associated ubiquitin-dependent protein catabolic process	5	6	1.926e-02
GO:BP	GO:0008654	phospholipid biosynthetic process	70	257	1.950e-02
GO:BP	GO:0009411	response to UV	46	155	1.950e-02
GO:BP	GO:0098910	regulation of atrial cardiac muscle cell action potential	4	4	1.950e-02
GO:BP	GO:0048597	post-embryonic camera-type eye morphogenesis	4	4	1.950e-02
GO:BP	GO:0035107	appendage morphogenesis	46	155	1.950e-02
GO:BP	GO:0035108	limb morphogenesis	46	155	1.950e-02
GO:BP	GO:1904506	negative regulation of telomere maintenance in response to DNA damage	4	4	1.950e-02
GO:BP	GO:0035879	plasma membrane lactate transport	4	4	1.950e-02
GO:BP	GO:1901698	response to nitrogen compound	249	1080	1.950e-02
GO:BP	GO:0060928	atrioventricular node cell development	4	4	1.950e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	51	176	1.978e-02
GO:BP	GO:0036258	multivesicular body assembly	14	32	1.979e-02
GO:BP	GO:1905820	positive regulation of chromosome separation	14	32	1.979e-02
GO:BP	GO:2000279	negative regulation of DNA biosynthetic process	14	32	1.979e-02
GO:BP	GO:0006997	nucleus organization	44	147	1.998e-02
GO:BP	GO:0006164	purine nucleotide biosynthetic process	55	193	2.004e-02
GO:BP	GO:0048488	synaptic vesicle endocytosis	28	83	2.015e-02
GO:BP	GO:0042594	response to starvation	61	219	2.109e-02
GO:BP	GO:0002183	cytoplasmic translational initiation	18	46	2.109e-02
GO:BP	GO:0031124	mRNA 3’-end processing	18	46	2.109e-02
GO:BP	GO:0042149	cellular response to glucose starvation	18	46	2.109e-02
GO:BP	GO:1905898	positive regulation of response to endoplasmic reticulum stress	16	39	2.110e-02
GO:BP	GO:0090174	organelle membrane fusion	38	123	2.145e-02
GO:BP	GO:0021915	neural tube development	47	160	2.146e-02
GO:BP	GO:1902414	protein localization to cell junction	37	119	2.154e-02
GO:BP	GO:0009134	nucleoside diphosphate catabolic process	34	107	2.166e-02
GO:BP	GO:0086011	membrane repolarization during action potential	13	29	2.181e-02
GO:BP	GO:0062028	regulation of stress granule assembly	7	11	2.187e-02
GO:BP	GO:0018195	peptidyl-arginine modification	7	11	2.187e-02
GO:BP	GO:0086070	SA node cell to atrial cardiac muscle cell communication	7	11	2.187e-02
GO:BP	GO:0009267	cellular response to starvation	51	177	2.204e-02
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	155	642	2.221e-02
GO:BP	GO:0140056	organelle localization by membrane tethering	26	76	2.282e-02
GO:BP	GO:0007019	microtubule depolymerization	19	50	2.332e-02
GO:BP	GO:0071985	multivesicular body sorting pathway	19	50	2.332e-02
GO:BP	GO:0042981	regulation of apoptotic process	328	1462	2.344e-02
GO:BP	GO:0006937	regulation of muscle contraction	48	165	2.369e-02
GO:BP	GO:0002026	regulation of the force of heart contraction	12	26	2.369e-02
GO:BP	GO:0033617	mitochondrial cytochrome c oxidase assembly	12	26	2.369e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	12	26	2.369e-02
GO:BP	GO:0031167	rRNA methylation	12	26	2.369e-02
GO:BP	GO:1900542	regulation of purine nucleotide metabolic process	28	84	2.393e-02
GO:BP	GO:0031667	response to nutrient levels	126	510	2.402e-02
GO:BP	GO:0032271	regulation of protein polymerization	56	199	2.412e-02
GO:BP	GO:0003206	cardiac chamber morphogenesis	38	124	2.452e-02
GO:BP	GO:0009135	purine nucleoside diphosphate metabolic process	36	116	2.491e-02
GO:BP	GO:0009179	purine ribonucleoside diphosphate metabolic process	36	116	2.491e-02
GO:BP	GO:0003283	atrial septum development	11	23	2.537e-02
GO:BP	GO:0015919	peroxisomal membrane transport	11	23	2.537e-02
GO:BP	GO:0046599	regulation of centriole replication	11	23	2.537e-02
GO:BP	GO:0043574	peroxisomal transport	11	23	2.537e-02
GO:BP	GO:0015780	nucleotide-sugar transmembrane transport	8	14	2.539e-02
GO:BP	GO:1904353	regulation of telomere capping	8	14	2.539e-02
GO:BP	GO:0006241	CTP biosynthetic process	8	14	2.539e-02
GO:BP	GO:0016925	protein sumoylation	24	69	2.539e-02
GO:BP	GO:0090559	regulation of membrane permeability	24	69	2.539e-02
GO:BP	GO:0002028	regulation of sodium ion transport	24	69	2.539e-02
GO:BP	GO:0043170	macromolecule metabolic process	2425	12048	2.593e-02
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	25	73	2.639e-02
GO:BP	GO:0044843	cell cycle G1/S phase transition	63	230	2.646e-02
GO:BP	GO:0036257	multivesicular body organization	14	33	2.661e-02
GO:BP	GO:0060421	positive regulation of heart growth	14	33	2.661e-02
GO:BP	GO:0051382	kinetochore assembly	9	17	2.663e-02
GO:BP	GO:0085020	protein K6-linked ubiquitination	9	17	2.663e-02
GO:BP	GO:0032786	positive regulation of DNA-templated transcription, elongation	21	58	2.675e-02
GO:BP	GO:0003151	outflow tract morphogenesis	26	77	2.704e-02
GO:BP	GO:0086091	regulation of heart rate by cardiac conduction	16	40	2.730e-02
GO:BP	GO:0034329	cell junction assembly	124	503	2.731e-02
GO:BP	GO:0031669	cellular response to nutrient levels	67	248	2.809e-02
GO:BP	GO:0051261	protein depolymerization	37	121	2.816e-02
GO:BP	GO:0006906	vesicle fusion	37	121	2.816e-02
GO:BP	GO:0006140	regulation of nucleotide metabolic process	28	85	2.816e-02
GO:BP	GO:0042391	regulation of membrane potential	114	458	2.842e-02
GO:BP	GO:1902117	positive regulation of organelle assembly	29	89	2.845e-02
GO:BP	GO:0000422	autophagy of mitochondrion	33	105	2.890e-02
GO:BP	GO:0060996	dendritic spine development	32	101	2.890e-02
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	42	142	2.991e-02
GO:BP	GO:0006520	amino acid metabolic process	78	297	2.991e-02
GO:BP	GO:1902108	regulation of mitochondrial membrane permeability involved in apoptotic process	17	44	3.075e-02
GO:BP	GO:0003208	cardiac ventricle morphogenesis	24	70	3.075e-02
GO:BP	GO:0099633	protein localization to postsynaptic specialization membrane	15	37	3.128e-02
GO:BP	GO:0099645	neurotransmitter receptor localization to postsynaptic specialization membrane	15	37	3.128e-02
GO:BP	GO:0006487	protein N-linked glycosylation	25	74	3.168e-02
GO:BP	GO:0051345	positive regulation of hydrolase activity	57	206	3.186e-02
GO:BP	GO:0010647	positive regulation of cell communication	395	1795	3.192e-02
GO:BP	GO:0006457	protein folding	60	219	3.203e-02
GO:BP	GO:0000447	endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	6	9	3.249e-02
GO:BP	GO:0036500	ATF6-mediated unfolded protein response	6	9	3.249e-02
GO:BP	GO:0023056	positive regulation of signaling	395	1796	3.296e-02
GO:BP	GO:0071480	cellular response to gamma radiation	12	27	3.296e-02
GO:BP	GO:0016233	telomere capping	12	27	3.296e-02
GO:BP	GO:0033119	negative regulation of RNA splicing	12	27	3.296e-02
GO:BP	GO:0010882	regulation of cardiac muscle contraction by calcium ion signaling	12	27	3.296e-02
GO:BP	GO:0032511	late endosome to vacuole transport via multivesicular body sorting pathway	12	27	3.296e-02
GO:BP	GO:0022406	membrane docking	28	86	3.307e-02
GO:BP	GO:0051049	regulation of transport	356	1607	3.307e-02
GO:BP	GO:0006900	vesicle budding from membrane	28	86	3.307e-02
GO:BP	GO:0016601	Rac protein signal transduction	18	48	3.333e-02
GO:BP	GO:0014020	primary neural tube formation	30	94	3.333e-02
GO:BP	GO:0045017	glycerolipid biosynthetic process	67	250	3.333e-02
GO:BP	GO:1990542	mitochondrial transmembrane transport	31	98	3.333e-02
GO:BP	GO:1904262	negative regulation of TORC1 signaling	18	48	3.333e-02
GO:BP	GO:0007032	endosome organization	31	98	3.333e-02
GO:BP	GO:0006754	ATP biosynthetic process	32	102	3.333e-02
GO:BP	GO:0043067	regulation of programmed cell death	335	1506	3.348e-02
GO:BP	GO:0007368	determination of left/right symmetry	41	139	3.413e-02
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	50	177	3.475e-02
GO:BP	GO:1902305	regulation of sodium ion transmembrane transport	16	41	3.501e-02
GO:BP	GO:0003203	endocardial cushion morphogenesis	16	41	3.501e-02
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	23	67	3.550e-02
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	11	24	3.591e-02
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	11	24	3.591e-02
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	11	24	3.591e-02
GO:BP	GO:0000423	mitophagy	24	71	3.654e-02
GO:BP	GO:0060322	head development	188	806	3.697e-02
GO:BP	GO:0009101	glycoprotein biosynthetic process	78	300	3.806e-02
GO:BP	GO:1901799	negative regulation of proteasomal protein catabolic process	20	56	3.808e-02
GO:BP	GO:0141137	positive regulation of gene expression, epigenetic	20	56	3.808e-02
GO:BP	GO:0016055	Wnt signaling pathway	113	458	3.808e-02
GO:BP	GO:0062237	protein localization to postsynapse	20	56	3.808e-02
GO:BP	GO:0032231	regulation of actin filament bundle assembly	32	103	3.830e-02
GO:BP	GO:1903573	negative regulation of response to endoplasmic reticulum stress	17	45	3.830e-02
GO:BP	GO:0003207	cardiac chamber formation	7	12	3.830e-02
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	32	103	3.830e-02
GO:BP	GO:0086067	AV node cell to bundle of His cell communication	7	12	3.830e-02
GO:BP	GO:0072662	protein localization to peroxisome	10	21	3.830e-02
GO:BP	GO:0009062	fatty acid catabolic process	33	107	3.830e-02
GO:BP	GO:1901661	quinone metabolic process	10	21	3.830e-02
GO:BP	GO:0051657	maintenance of organelle location	7	12	3.830e-02
GO:BP	GO:0072710	response to hydroxyurea	7	12	3.830e-02
GO:BP	GO:0032388	positive regulation of intracellular transport	41	140	3.830e-02
GO:BP	GO:0008637	apoptotic mitochondrial changes	32	103	3.830e-02
GO:BP	GO:0097061	dendritic spine organization	27	83	3.830e-02
GO:BP	GO:0046051	UTP metabolic process	7	12	3.830e-02
GO:BP	GO:0046928	regulation of neurotransmitter secretion	27	83	3.830e-02
GO:BP	GO:0036465	synaptic vesicle recycling	30	95	3.830e-02
GO:BP	GO:0072663	establishment of protein localization to peroxisome	10	21	3.830e-02
GO:BP	GO:0006285	base-excision repair, AP site formation	7	12	3.830e-02
GO:BP	GO:0099188	postsynaptic cytoskeleton organization	10	21	3.830e-02
GO:BP	GO:0060623	regulation of chromosome condensation	7	12	3.830e-02
GO:BP	GO:0009261	ribonucleotide catabolic process	40	136	3.873e-02
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	49	174	3.908e-02
GO:BP	GO:1900101	regulation of endoplasmic reticulum unfolded protein response	13	31	3.910e-02
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	13	31	3.910e-02
GO:BP	GO:0060997	dendritic spine morphogenesis	21	60	3.910e-02
GO:BP	GO:1904294	positive regulation of ERAD pathway	9	18	4.006e-02
GO:BP	GO:0001522	pseudouridine synthesis	9	18	4.006e-02
GO:BP	GO:0043244	regulation of protein-containing complex disassembly	38	128	4.016e-02
GO:BP	GO:0090306	meiotic spindle assembly	8	15	4.051e-02
GO:BP	GO:0023057	negative regulation of signaling	319	1435	4.134e-02
GO:BP	GO:0150116	regulation of cell-substrate junction organization	23	68	4.185e-02
GO:BP	GO:0035825	homologous recombination	23	68	4.185e-02
GO:BP	GO:0032007	negative regulation of TOR signaling	23	68	4.185e-02
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	34	112	4.287e-02
GO:BP	GO:0043149	stress fiber assembly	33	108	4.336e-02
GO:BP	GO:0030038	contractile actin filament bundle assembly	33	108	4.336e-02
GO:BP	GO:0036297	interstrand cross-link repair	16	42	4.403e-02
GO:BP	GO:0099558	maintenance of synapse structure	12	28	4.415e-02
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	12	28	4.415e-02
GO:BP	GO:0003209	cardiac atrium morphogenesis	12	28	4.415e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	29	92	4.446e-02
GO:BP	GO:0031114	regulation of microtubule depolymerization	14	35	4.547e-02
GO:BP	GO:1902410	mitotic cytokinetic process	14	35	4.547e-02
GO:BP	GO:0009154	purine ribonucleotide catabolic process	38	129	4.565e-02
GO:BP	GO:0006370	7-methylguanosine mRNA capping	5	7	4.565e-02
GO:BP	GO:0051204	protein insertion into mitochondrial membrane	5	7	4.565e-02
GO:BP	GO:1990048	anterograde neuronal dense core vesicle transport	5	7	4.565e-02
GO:BP	GO:1903436	regulation of mitotic cytokinetic process	5	7	4.565e-02
GO:BP	GO:0086028	bundle of His cell to Purkinje myocyte signaling	5	7	4.565e-02
GO:BP	GO:0086043	bundle of His cell action potential	5	7	4.565e-02
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	57	210	4.565e-02
GO:BP	GO:0032954	regulation of cytokinetic process	5	7	4.565e-02
GO:BP	GO:0046048	UDP metabolic process	5	7	4.565e-02
GO:BP	GO:0099545	trans-synaptic signaling by trans-synaptic complex	5	7	4.565e-02
GO:BP	GO:0018023	peptidyl-lysine trimethylation	5	7	4.565e-02
GO:BP	GO:1903438	positive regulation of mitotic cytokinetic process	5	7	4.565e-02
GO:BP	GO:0017183	protein histidyl modification to diphthamide	5	7	4.565e-02
GO:BP	GO:0009193	pyrimidine ribonucleoside diphosphate metabolic process	5	7	4.565e-02
GO:BP	GO:0035735	intraciliary transport involved in cilium assembly	5	7	4.565e-02
GO:BP	GO:0035617	stress granule disassembly	5	7	4.565e-02
GO:BP	GO:0060972	left/right pattern formation	42	146	4.637e-02
GO:BP	GO:0006119	oxidative phosphorylation	42	146	4.637e-02
GO:BP	GO:0003254	regulation of membrane depolarization	17	46	4.702e-02
GO:BP	GO:0007020	microtubule nucleation	17	46	4.702e-02
GO:BP	GO:0001932	regulation of protein phosphorylation	181	779	4.773e-02
GO:BP	GO:0040029	epigenetic regulation of gene expression	77	299	4.840e-02
GO:BP	GO:0035020	regulation of Rac protein signal transduction	11	25	4.845e-02
GO:BP	GO:0035994	response to muscle stretch	11	25	4.845e-02
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	11	25	4.845e-02
GO:BP	GO:0030813	positive regulation of nucleotide catabolic process	11	25	4.845e-02
GO:BP	GO:0090231	regulation of spindle checkpoint	11	25	4.845e-02
GO:BP	GO:1901028	regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	11	25	4.845e-02
GO:BP	GO:0033123	positive regulation of purine nucleotide catabolic process	11	25	4.845e-02
GO:BP	GO:0045821	positive regulation of glycolytic process	11	25	4.845e-02
GO:BP	GO:0016445	somatic diversification of immunoglobulins	23	69	4.914e-02
GO:BP	GO:0001578	microtubule bundle formation	39	134	4.958e-02
GO:BP	GO:0001841	neural tube formation	31	101	4.970e-02
GO:BP	GO:0170036	import into the mitochondrion	18	50	4.970e-02
GO:BP	GO:0061371	determination of heart left/right asymmetry	24	73	4.970e-02
GO:BP	GO:0010648	negative regulation of cell communication	318	1436	4.970e-02
GO:BP	GO:0003281	ventricular septum development	24	73	4.970e-02
GO:BP	GO:0032467	positive regulation of cytokinesis	18	50	4.970e-02
KEGG	KEGG:00970	Aminoacyl-tRNA biosynthesis	27	44	6.758e-06
KEGG	KEGG:05168	Herpes simplex virus 1 infection	162	506	8.870e-06
KEGG	KEGG:03018	RNA degradation	38	79	2.840e-05
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	55	140	2.147e-04
KEGG	KEGG:03082	ATP-dependent chromatin remodeling	46	116	8.407e-04
KEGG	KEGG:04110	Cell cycle	55	157	5.361e-03
KEGG	KEGG:03440	Homologous recombination	20	41	5.361e-03
KEGG	KEGG:03410	Base excision repair	21	44	5.361e-03
KEGG	KEGG:03040	Spliceosome	60	174	5.361e-03
KEGG	KEGG:04137	Mitophagy - animal	38	103	1.192e-02
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	56	168	1.192e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	107	363	1.192e-02
KEGG	KEGG:04130	SNARE interactions in vesicular transport	16	32	1.192e-02
KEGG	KEGG:03013	Nucleocytoplasmic transport	39	108	1.345e-02
KEGG	KEGG:00240	Pyrimidine metabolism	23	57	3.113e-02

#write.csv(table_DOX24R_down_genes, "output/table_DOX24R_downreg_genes.csv")

#GO:BP
table_DOX24Tshare_down_genes_GOBP <- table_DOX24Tshare_down_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

#saveRDS(table_motif1_GOBP_d, "data/table_motif1_GOBP_d.RDS")

table_DOX24Tshare_down_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared Down DEGs Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-11.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX24Tshare_down_genes_KEGG <- table_DOX24Tshare_down_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24Tshare_down_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared Down DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of Down-12.png

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###RUVs GO/KEGG for All Conditions

#####DOX24 Genes Specific#####
D24_DEGs_mat_RUV <- as.matrix(DOX24T_DEGs_GO_RUV)
D24_DEGs_vec_RUV <- as.character(DOX24T_DEGs_GO_RUV$Entrez_ID)

#saveRDS(D24_DEGs_mat_RUV, "data/new/RUV/D24_DEGs_mat_RUV.RDS")

DOX_24_dxr_gene_RUV <- gost(query = D24_DEGs_vec_RUV,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

#check if there are any KEGG terms popping up
unique(DOX_24_dxr_gene_RUV$result$source)

[1] "GO:BP"

#only GO:BP appearing

DOX_24_gost_genes_RUV <- gostplot(DOX_24_dxr_gene_RUV, capped = FALSE, interactive = TRUE)
DOX_24_gost_genes_RUV

table_DOX24_genes_RUV <- DOX_24_dxr_gene_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0048518	positive regulation of biological process	353	6264	1.727e-07
GO:BP	GO:0080090	regulation of primary metabolic process	313	5390	1.727e-07
GO:BP	GO:0048522	positive regulation of cellular process	335	5920	3.353e-07
GO:BP	GO:0065007	biological regulation	617	12743	1.482e-05
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	233	3990	3.463e-05
GO:BP	GO:0051252	regulation of RNA metabolic process	218	3687	3.463e-05
GO:BP	GO:0050794	regulation of cellular process	581	11946	3.463e-05
GO:BP	GO:0050789	regulation of biological process	597	12336	3.463e-05
GO:BP	GO:0006351	DNA-templated transcription	209	3549	8.673e-05
GO:BP	GO:0006355	regulation of DNA-templated transcription	201	3409	1.245e-04
GO:BP	GO:0051128	regulation of cellular component organization	153	2433	1.245e-04
GO:BP	GO:2001141	regulation of RNA biosynthetic process	201	3428	1.717e-04
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	108	1588	2.373e-04
GO:BP	GO:0030030	cell projection organization	110	1631	2.565e-04
GO:BP	GO:0019538	protein metabolic process	260	4721	3.103e-04
GO:BP	GO:0007049	cell cycle	111	1663	3.283e-04
GO:BP	GO:0006366	transcription by RNA polymerase II	163	2711	4.684e-04
GO:BP	GO:1903047	mitotic cell cycle process	60	745	4.684e-04
GO:BP	GO:0051726	regulation of cell cycle	79	1087	5.400e-04
GO:BP	GO:0043412	macromolecule modification	178	3030	5.400e-04
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	153	2578	1.815e-03
GO:BP	GO:0009056	catabolic process	156	2639	1.815e-03
GO:BP	GO:0022402	cell cycle process	87	1280	1.966e-03
GO:BP	GO:0033554	cellular response to stress	115	1830	2.408e-03
GO:BP	GO:0000278	mitotic cell cycle	65	892	3.346e-03
GO:BP	GO:0009057	macromolecule catabolic process	93	1417	3.352e-03
GO:BP	GO:0019222	regulation of metabolic process	355	7035	3.845e-03
GO:BP	GO:0051716	cellular response to stimulus	370	7376	3.845e-03
GO:BP	GO:0060255	regulation of macromolecule metabolic process	331	6492	3.845e-03
GO:BP	GO:0051641	cellular localization	202	3661	3.987e-03
GO:BP	GO:0035556	intracellular signal transduction	169	2965	3.987e-03
GO:BP	GO:0007275	multicellular organism development	250	4727	5.918e-03
GO:BP	GO:0036211	protein modification process	162	2846	6.255e-03
GO:BP	GO:0060021	roof of mouth development	14	94	7.333e-03
GO:BP	GO:0048731	system development	218	4053	7.688e-03
GO:BP	GO:0006402	mRNA catabolic process	26	261	8.420e-03
GO:BP	GO:0141188	nucleic acid catabolic process	31	343	1.034e-02
GO:BP	GO:0016055	Wnt signaling pathway	38	458	1.034e-02
GO:BP	GO:0048523	negative regulation of cellular process	288	5629	1.133e-02
GO:BP	GO:0048762	mesenchymal cell differentiation	25	252	1.133e-02
GO:BP	GO:0006401	RNA catabolic process	29	315	1.170e-02
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	8	35	1.248e-02
GO:BP	GO:0001967	suckling behavior	5	12	1.248e-02
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	42	535	1.290e-02
GO:BP	GO:0007507	heart development	46	605	1.290e-02
GO:BP	GO:0140639	positive regulation of pyroptotic inflammatory response	4	7	1.310e-02
GO:BP	GO:0060485	mesenchyme development	29	320	1.310e-02
GO:BP	GO:0051254	positive regulation of RNA metabolic process	110	1835	1.310e-02
GO:BP	GO:0060039	pericardium development	6	19	1.310e-02
GO:BP	GO:0061013	regulation of mRNA catabolic process	21	198	1.310e-02
GO:BP	GO:0006996	organelle organization	194	3594	1.330e-02
GO:BP	GO:0033043	regulation of organelle organization	75	1148	1.373e-02
GO:BP	GO:0006974	DNA damage response	62	908	1.598e-02
GO:BP	GO:0051649	establishment of localization in cell	118	2010	1.598e-02
GO:BP	GO:0051246	regulation of protein metabolic process	110	1855	1.754e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	65	970	1.754e-02
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	286	5644	1.754e-02
GO:BP	GO:0009893	positive regulation of metabolic process	193	3597	1.754e-02
GO:BP	GO:0044770	cell cycle phase transition	41	532	1.758e-02
GO:BP	GO:0048519	negative regulation of biological process	294	5834	1.835e-02
GO:BP	GO:0007399	nervous system development	146	2604	1.835e-02
GO:BP	GO:0042475	odontogenesis of dentin-containing tooth	13	95	1.835e-02
GO:BP	GO:0044238	primary metabolic process	572	12342	1.848e-02
GO:BP	GO:0009653	anatomical structure morphogenesis	151	2713	1.866e-02
GO:BP	GO:0043487	regulation of RNA stability	20	193	1.996e-02
GO:BP	GO:0010468	regulation of gene expression	280	5536	2.115e-02
GO:BP	GO:0006950	response to stress	208	3948	2.181e-02
GO:BP	GO:0048666	neuron development	75	1177	2.252e-02
GO:BP	GO:0007166	cell surface receptor signaling pathway	155	2819	2.382e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	177	3288	2.382e-02
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	101	1699	2.382e-02
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	101	1697	2.382e-02
GO:BP	GO:0098813	nuclear chromosome segregation	28	323	2.382e-02
GO:BP	GO:0061635	regulation of protein complex stability	5	15	2.433e-02
GO:BP	GO:0072359	circulatory system development	73	1145	2.433e-02
GO:BP	GO:0048863	stem cell differentiation	23	245	2.437e-02
GO:BP	GO:0060979	vasculogenesis involved in coronary vascular morphogenesis	3	4	2.437e-02
GO:BP	GO:0006574	valine catabolic process	3	4	2.437e-02
GO:BP	GO:0009889	regulation of biosynthetic process	291	5809	2.437e-02
GO:BP	GO:0000302	response to reactive oxygen species	20	199	2.437e-02
GO:BP	GO:0048856	anatomical structure development	299	5997	2.592e-02
GO:BP	GO:0045786	negative regulation of cell cycle	31	377	2.592e-02
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	92	1529	2.668e-02
GO:BP	GO:1903311	regulation of mRNA metabolic process	27	312	2.715e-02
GO:BP	GO:0044782	cilium organization	34	431	2.832e-02
GO:BP	GO:0009966	regulation of signal transduction	164	3034	2.890e-02
GO:BP	GO:0051129	negative regulation of cellular component organization	49	701	2.890e-02
GO:BP	GO:0003214	cardiac left ventricle morphogenesis	5	16	2.890e-02
GO:BP	GO:0010564	regulation of cell cycle process	50	720	2.905e-02
GO:BP	GO:0060271	cilium assembly	32	403	3.510e-02
GO:BP	GO:0061564	axon development	39	528	3.778e-02
GO:BP	GO:0030182	neuron differentiation	87	1451	3.906e-02
GO:BP	GO:0065009	regulation of molecular function	89	1496	3.921e-02
GO:BP	GO:0009987	cellular process	871	20247	3.921e-02
GO:BP	GO:0001822	kidney development	27	322	3.921e-02
GO:BP	GO:2000178	negative regulation of neural precursor cell proliferation	6	26	3.921e-02
GO:BP	GO:0006399	tRNA metabolic process	20	210	3.921e-02
GO:BP	GO:0048207	vesicle targeting, rough ER to cis-Golgi	6	26	3.921e-02
GO:BP	GO:0051179	localization	277	5555	3.921e-02
GO:BP	GO:0031344	regulation of cell projection organization	46	658	3.921e-02
GO:BP	GO:0048699	generation of neurons	91	1536	3.921e-02
GO:BP	GO:0048208	COPII vesicle coating	6	26	3.921e-02
GO:BP	GO:0007059	chromosome segregation	33	427	3.954e-02
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	74	1199	3.954e-02
GO:BP	GO:0120161	regulation of cold-induced thermogenesis	16	151	3.954e-02
GO:BP	GO:1901987	regulation of cell cycle phase transition	33	427	3.954e-02
GO:BP	GO:0031175	neuron projection development	65	1023	3.954e-02
GO:BP	GO:0003208	cardiac ventricle morphogenesis	10	70	3.954e-02
GO:BP	GO:0043488	regulation of mRNA stability	18	181	3.954e-02
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	55	831	3.954e-02
GO:BP	GO:0051253	negative regulation of RNA metabolic process	84	1400	3.954e-02
GO:BP	GO:0060029	convergent extension involved in organogenesis	3	5	4.022e-02
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	8	47	4.022e-02
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	115	2036	4.022e-02
GO:BP	GO:0010646	regulation of cell communication	183	3486	4.039e-02
GO:BP	GO:0001503	ossification	33	430	4.053e-02
GO:BP	GO:0060070	canonical Wnt signaling pathway	26	311	4.102e-02
GO:BP	GO:0106106	cold-induced thermogenesis	16	153	4.102e-02
GO:BP	GO:0006508	proteolysis	88	1486	4.102e-02
GO:BP	GO:0022008	neurogenesis	102	1771	4.102e-02
GO:BP	GO:0030031	cell projection assembly	43	613	4.354e-02
GO:BP	GO:0023051	regulation of signaling	182	3478	4.581e-02
GO:BP	GO:0035239	tube morphogenesis	57	879	4.581e-02
GO:BP	GO:1990845	adaptive thermogenesis	17	170	4.582e-02
GO:BP	GO:0000902	cell morphogenesis	63	996	4.611e-02
GO:BP	GO:0072001	renal system development	27	332	4.696e-02
GO:BP	GO:0140014	mitotic nuclear division	24	282	4.711e-02
GO:BP	GO:0009967	positive regulation of signal transduction	92	1578	4.745e-02
GO:BP	GO:0003007	heart morphogenesis	23	266	4.745e-02
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	42	600	4.793e-02
GO:BP	GO:0000819	sister chromatid segregation	21	234	4.793e-02
GO:BP	GO:0007346	regulation of mitotic cell cycle	36	492	4.959e-02

#GO:BP
table_DOX24_genes_GOBP_RUV <- table_DOX24_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))


table_DOX24_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Specific DEGs Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# #KEGG - no KEGG terms popped up for this one?
# table_DOX24_genes_KEGG_RUV <- table_DOX24_genes_RUV %>% 
#   dplyr::filter(source=="KEGG") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX24_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX24T Specific DEGs Enriched KEGG Terms RUVs")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("KEGG term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))


#####DOX24T shared DEGs GO KEGG#####
D24Tshare_DEGs_mat_RUV <- as.matrix(DOX24T_share_DEGs_GO_plot_RUV)

DOX_24Tshare_dxr_gene_RUV <- gost(query = D24Tshare_DEGs_mat_RUV,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

#check if there are any KEGG terms popping up
unique(DOX_24Tshare_dxr_gene_RUV$result$source)

[1] "GO:BP"

#only GO:BP appearing

DOX_24Tshare_gost_genes_RUV <- 
  gostplot(DOX_24Tshare_dxr_gene_RUV, capped = FALSE, interactive = TRUE)
DOX_24Tshare_gost_genes_RUV

table_DOX24Tshare_genes_RUV <- DOX_24Tshare_dxr_gene_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24Tshare_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0006996	organelle organization	291	3594	4.937e-10
GO:BP	GO:0035556	intracellular signal transduction	249	2965	6.072e-10
GO:BP	GO:0080090	regulation of primary metabolic process	389	5390	5.622e-08
GO:BP	GO:0051179	localization	398	5555	5.869e-08
GO:BP	GO:0019538	protein metabolic process	346	4721	1.339e-07
GO:BP	GO:0048518	positive regulation of biological process	434	6264	3.250e-07
GO:BP	GO:0051649	establishment of localization in cell	173	2010	3.250e-07
GO:BP	GO:0051641	cellular localization	278	3661	3.991e-07
GO:BP	GO:0006810	transport	322	4407	7.021e-07
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	296	3990	7.212e-07
GO:BP	GO:0009893	positive regulation of metabolic process	272	3597	7.212e-07
GO:BP	GO:0048522	positive regulation of cellular process	411	5920	7.212e-07
GO:BP	GO:0051252	regulation of RNA metabolic process	277	3687	8.117e-07
GO:BP	GO:0023051	regulation of signaling	263	3478	1.246e-06
GO:BP	GO:0009056	catabolic process	210	2639	1.330e-06
GO:BP	GO:0046907	intracellular transport	126	1381	1.706e-06
GO:BP	GO:0010646	regulation of cell communication	262	3486	2.013e-06
GO:BP	GO:0032502	developmental process	443	6553	2.464e-06
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	249	3288	2.523e-06
GO:BP	GO:0009966	regulation of signal transduction	232	3034	4.014e-06
GO:BP	GO:0141124	intracellular signaling cassette	160	1912	4.014e-06
GO:BP	GO:0009894	regulation of catabolic process	100	1040	4.365e-06
GO:BP	GO:0050789	regulation of biological process	755	12336	7.218e-06
GO:BP	GO:0065007	biological regulation	776	12743	7.325e-06
GO:BP	GO:0048856	anatomical structure development	407	5997	7.864e-06
GO:BP	GO:0051128	regulation of cellular component organization	192	2433	8.227e-06
GO:BP	GO:0007275	multicellular organism development	332	4727	9.381e-06
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	166	2036	9.381e-06
GO:BP	GO:0009896	positive regulation of catabolic process	61	546	1.612e-05
GO:BP	GO:0050794	regulation of cellular process	731	11946	1.927e-05
GO:BP	GO:0051234	establishment of localization	341	4928	2.406e-05
GO:BP	GO:0033036	macromolecule localization	239	3228	2.406e-05
GO:BP	GO:0033043	regulation of organelle organization	104	1148	3.044e-05
GO:BP	GO:0048731	system development	288	4053	3.283e-05
GO:BP	GO:0051254	positive regulation of RNA metabolic process	150	1835	3.283e-05
GO:BP	GO:0006351	DNA-templated transcription	257	3549	4.024e-05
GO:BP	GO:0007032	endosome organization	20	98	4.695e-05
GO:BP	GO:0009057	macromolecule catabolic process	121	1417	5.892e-05
GO:BP	GO:2001141	regulation of RNA biosynthetic process	248	3428	7.138e-05
GO:BP	GO:0016192	vesicle-mediated transport	132	1592	7.990e-05
GO:BP	GO:0006355	regulation of DNA-templated transcription	246	3409	9.463e-05
GO:BP	GO:0032880	regulation of protein localization	84	907	1.636e-04
GO:BP	GO:0033554	cellular response to stress	146	1830	1.636e-04
GO:BP	GO:0070727	cellular macromolecule localization	206	2782	1.660e-04
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	126	1529	1.839e-04
GO:BP	GO:0051716	cellular response to stimulus	474	7376	1.935e-04
GO:BP	GO:0060341	regulation of cellular localization	91	1013	1.935e-04
GO:BP	GO:0019222	regulation of metabolic process	454	7035	2.394e-04
GO:BP	GO:1902473	regulation of protein localization to synapse	10	29	2.416e-04
GO:BP	GO:0048583	regulation of response to stimulus	278	3993	2.468e-04
GO:BP	GO:0042254	ribosome biogenesis	39	323	3.382e-04
GO:BP	GO:0051253	negative regulation of RNA metabolic process	116	1400	3.396e-04
GO:BP	GO:0008104	protein localization	203	2770	3.433e-04
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	191	2578	3.562e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	67	692	3.734e-04
GO:BP	GO:0016072	rRNA metabolic process	34	266	3.844e-04
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	135	1699	4.088e-04
GO:BP	GO:0043412	macromolecule modification	218	3030	4.486e-04
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	63	643	4.696e-04
GO:BP	GO:0043009	chordate embryonic development	65	671	4.737e-04
GO:BP	GO:0051640	organelle localization	61	620	5.398e-04
GO:BP	GO:0071495	cellular response to endogenous stimulus	103	1223	5.398e-04
GO:BP	GO:0006364	rRNA processing	30	225	5.398e-04
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	134	1697	5.398e-04
GO:BP	GO:0023052	signaling	421	6515	5.398e-04
GO:BP	GO:0032879	regulation of localization	155	2029	5.797e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	150	1953	6.120e-04
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	190	2593	6.120e-04
GO:BP	GO:0007399	nervous system development	190	2604	7.862e-04
GO:BP	GO:0033044	regulation of chromosome organization	31	242	7.940e-04
GO:BP	GO:0070925	organelle assembly	90	1046	8.425e-04
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	72	786	8.643e-04
GO:BP	GO:0006366	transcription by RNA polymerase II	196	2711	9.123e-04
GO:BP	GO:0071705	nitrogen compound transport	147	1923	9.123e-04
GO:BP	GO:0007154	cell communication	420	6540	9.269e-04
GO:BP	GO:0061024	membrane organization	74	821	1.077e-03
GO:BP	GO:0019941	modification-dependent protein catabolic process	61	638	1.091e-03
GO:BP	GO:0061919	process utilizing autophagic mechanism	58	597	1.091e-03
GO:BP	GO:0006914	autophagy	58	597	1.091e-03
GO:BP	GO:0009891	positive regulation of biosynthetic process	194	2696	1.254e-03
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	60	628	1.254e-03
GO:BP	GO:0016050	vesicle organization	41	376	1.462e-03
GO:BP	GO:0048513	animal organ development	217	3085	1.527e-03
GO:BP	GO:1990778	protein localization to cell periphery	40	365	1.605e-03
GO:BP	GO:0051246	regulation of protein metabolic process	141	1855	1.629e-03
GO:BP	GO:0016197	endosomal transport	34	290	1.635e-03
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	81	938	1.730e-03
GO:BP	GO:1902414	protein localization to cell junction	19	119	1.738e-03
GO:BP	GO:0009790	embryo development	94	1135	1.921e-03
GO:BP	GO:0071840	cellular component organization or biogenesis	520	8393	1.973e-03
GO:BP	GO:0010498	proteasomal protein catabolic process	53	543	1.973e-03
GO:BP	GO:0015031	protein transport	114	1444	2.087e-03
GO:BP	GO:0060996	dendritic spine development	17	101	2.174e-03
GO:BP	GO:0051656	establishment of organelle localization	49	491	2.174e-03
GO:BP	GO:0051276	chromosome organization	55	574	2.235e-03
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	14	73	2.403e-03
GO:BP	GO:0051247	positive regulation of protein metabolic process	87	1039	2.404e-03
GO:BP	GO:0006974	DNA damage response	78	908	2.613e-03
GO:BP	GO:0006950	response to stress	266	3948	2.794e-03
GO:BP	GO:0031503	protein-containing complex localization	27	215	2.950e-03
GO:BP	GO:0097500	receptor localization to non-motile cilium	4	5	2.950e-03
GO:BP	GO:0010639	negative regulation of organelle organization	38	352	2.950e-03
GO:BP	GO:0060255	regulation of macromolecule metabolic process	411	6492	3.822e-03
GO:BP	GO:0051301	cell division	60	658	3.822e-03
GO:BP	GO:0036211	protein modification process	199	2846	4.177e-03
GO:BP	GO:0001701	in utero embryonic development	42	413	4.608e-03
GO:BP	GO:0006796	phosphate-containing compound metabolic process	172	2407	4.648e-03
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	42	414	4.777e-03
GO:BP	GO:0006793	phosphorus metabolic process	172	2410	4.829e-03
GO:BP	GO:0140352	export from cell	78	928	4.829e-03
GO:BP	GO:0050896	response to stimulus	549	8999	4.844e-03
GO:BP	GO:0007004	telomere maintenance via telomerase	12	60	4.883e-03
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	102	1296	5.102e-03
GO:BP	GO:0042592	homeostatic process	130	1736	5.102e-03
GO:BP	GO:0035418	protein localization to synapse	15	89	5.102e-03
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	101	1280	5.102e-03
GO:BP	GO:0051650	establishment of vesicle localization	25	200	5.208e-03
GO:BP	GO:0009653	anatomical structure morphogenesis	190	2713	5.208e-03
GO:BP	GO:0048519	negative regulation of biological process	372	5834	5.279e-03
GO:BP	GO:0048285	organelle fission	48	500	5.353e-03
GO:BP	GO:0009719	response to endogenous stimulus	114	1489	5.729e-03
GO:BP	GO:0007165	signal transduction	381	6002	5.918e-03
GO:BP	GO:0060322	head development	69	806	6.498e-03
GO:BP	GO:0007417	central nervous system development	86	1061	6.507e-03
GO:BP	GO:1902683	regulation of receptor localization to synapse	8	29	6.531e-03
GO:BP	GO:1905870	positive regulation of 3’-UTR-mediated mRNA stabilization	4	6	6.855e-03
GO:BP	GO:0065008	regulation of biological quality	203	2947	6.856e-03
GO:BP	GO:0048523	negative regulation of cellular process	359	5629	6.961e-03
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	12	63	6.961e-03
GO:BP	GO:0001889	liver development	20	147	7.373e-03
GO:BP	GO:0043112	receptor metabolic process	13	73	7.373e-03
GO:BP	GO:0007166	cell surface receptor signaling pathway	195	2819	7.373e-03
GO:BP	GO:0031401	positive regulation of protein modification process	57	637	7.540e-03
GO:BP	GO:0050793	regulation of developmental process	173	2457	7.616e-03
GO:BP	GO:0051648	vesicle localization	26	219	7.803e-03
GO:BP	GO:0140014	mitotic nuclear division	31	282	7.890e-03
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	33	308	7.928e-03
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	98	1256	8.057e-03
GO:BP	GO:2001252	positive regulation of chromosome organization	16	105	8.511e-03
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	19	138	8.593e-03
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	18	127	8.672e-03
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	15	95	8.833e-03
GO:BP	GO:0061008	hepaticobiliary system development	20	150	8.929e-03
GO:BP	GO:0030163	protein catabolic process	83	1030	8.929e-03
GO:BP	GO:0009968	negative regulation of signal transduction	102	1326	9.474e-03
GO:BP	GO:1903311	regulation of mRNA metabolic process	33	312	9.474e-03
GO:BP	GO:0006753	nucleoside phosphate metabolic process	57	646	9.833e-03
GO:BP	GO:0007264	small GTPase-mediated signal transduction	47	505	1.056e-02
GO:BP	GO:0009889	regulation of biosynthetic process	367	5809	1.059e-02
GO:BP	GO:0006401	RNA catabolic process	33	315	1.101e-02
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	49	535	1.119e-02
GO:BP	GO:0033365	protein localization to organelle	94	1209	1.128e-02
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	22	177	1.135e-02
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	118	1588	1.137e-02
GO:BP	GO:1905038	regulation of membrane lipid metabolic process	6	18	1.226e-02
GO:BP	GO:0043084	penile erection	4	7	1.226e-02
GO:BP	GO:0002328	pro-B cell differentiation	5	12	1.226e-02
GO:BP	GO:1903441	protein localization to ciliary membrane	5	12	1.226e-02
GO:BP	GO:1990456	mitochondrion-endoplasmic reticulum membrane tethering	4	7	1.226e-02
GO:BP	GO:0000278	mitotic cell cycle	73	892	1.250e-02
GO:BP	GO:0055088	lipid homeostasis	21	167	1.261e-02
GO:BP	GO:0019637	organophosphate metabolic process	85	1077	1.309e-02
GO:BP	GO:0051338	regulation of transferase activity	46	498	1.319e-02
GO:BP	GO:1903047	mitotic cell cycle process	63	745	1.338e-02
GO:BP	GO:0051129	negative regulation of cellular component organization	60	701	1.346e-02
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	29	268	1.362e-02
GO:BP	GO:0030030	cell projection organization	120	1631	1.371e-02
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	356	5644	1.412e-02
GO:BP	GO:0032940	secretion by cell	70	854	1.505e-02
GO:BP	GO:0030522	intracellular receptor signaling pathway	37	377	1.534e-02
GO:BP	GO:0098696	regulation of neurotransmitter receptor localization to postsynaptic specialization membrane	6	19	1.573e-02
GO:BP	GO:0140058	neuron projection arborization	8	34	1.578e-02
GO:BP	GO:0090407	organophosphate biosynthetic process	54	619	1.607e-02
GO:BP	GO:0007507	heart development	53	605	1.632e-02
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	18	136	1.646e-02
GO:BP	GO:0033143	regulation of intracellular steroid hormone receptor signaling pathway	12	71	1.646e-02
GO:BP	GO:2000303	regulation of ceramide biosynthetic process	5	13	1.688e-02
GO:BP	GO:0071897	DNA biosynthetic process	21	172	1.688e-02
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	21	172	1.688e-02
GO:BP	GO:0097499	protein localization to non-motile cilium	5	13	1.688e-02
GO:BP	GO:0048869	cellular developmental process	286	4438	1.717e-02
GO:BP	GO:0006402	mRNA catabolic process	28	261	1.798e-02
GO:BP	GO:0010508	positive regulation of autophagy	20	161	1.801e-02
GO:BP	GO:0016233	telomere capping	7	27	1.812e-02
GO:BP	GO:0030325	adrenal gland development	7	27	1.812e-02
GO:BP	GO:0042274	ribosomal small subunit biogenesis	15	104	1.842e-02
GO:BP	GO:0000280	nuclear division	42	452	1.842e-02
GO:BP	GO:0044238	primary metabolic process	721	12342	1.858e-02
GO:BP	GO:0051239	regulation of multicellular organismal process	199	2956	1.876e-02
GO:BP	GO:1905868	regulation of 3’-UTR-mediated mRNA stabilization	4	8	1.933e-02
GO:BP	GO:2000973	regulation of pro-B cell differentiation	4	8	1.933e-02
GO:BP	GO:0141188	nucleic acid catabolic process	34	343	1.935e-02
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	15	105	1.970e-02
GO:BP	GO:0001501	skeletal system development	48	540	1.970e-02
GO:BP	GO:0071396	cellular response to lipid	53	613	1.975e-02
GO:BP	GO:0007224	smoothened signaling pathway	19	151	1.975e-02
GO:BP	GO:0006403	RNA localization	23	200	1.991e-02
GO:BP	GO:0030154	cell differentiation	285	4437	1.999e-02
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	57	673	2.021e-02
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	24	213	2.021e-02
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	13	84	2.027e-02
GO:BP	GO:0044772	mitotic cell cycle phase transition	40	428	2.045e-02
GO:BP	GO:0046903	secretion	78	992	2.057e-02
GO:BP	GO:0022008	neurogenesis	127	1771	2.082e-02
GO:BP	GO:1901699	cellular response to nitrogen compound	55	645	2.082e-02
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	11	64	2.096e-02
GO:BP	GO:0023057	negative regulation of signaling	106	1435	2.144e-02
GO:BP	GO:0090153	regulation of sphingolipid biosynthetic process	5	14	2.144e-02
GO:BP	GO:0031860	telomeric 3’ overhang formation	3	4	2.144e-02
GO:BP	GO:0016482	cytosolic transport	18	141	2.144e-02
GO:BP	GO:0000209	protein polyubiquitination	29	280	2.201e-02
GO:BP	GO:0010468	regulation of gene expression	347	5536	2.232e-02
GO:BP	GO:0032543	mitochondrial translation	17	130	2.243e-02
GO:BP	GO:1903539	protein localization to postsynaptic membrane	10	55	2.243e-02
GO:BP	GO:0051094	positive regulation of developmental process	100	1343	2.289e-02
GO:BP	GO:0016358	dendrite development	26	242	2.309e-02
GO:BP	GO:0007420	brain development	62	754	2.309e-02
GO:BP	GO:0008219	cell death	140	1991	2.309e-02
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	25	230	2.437e-02
GO:BP	GO:0098813	nuclear chromosome segregation	32	323	2.456e-02
GO:BP	GO:0062237	protein localization to postsynapse	10	56	2.518e-02
GO:BP	GO:0032870	cellular response to hormone stimulus	54	638	2.552e-02
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	51	594	2.564e-02
GO:BP	GO:1905475	regulation of protein localization to membrane	22	193	2.567e-02
GO:BP	GO:0043487	regulation of RNA stability	22	193	2.567e-02
GO:BP	GO:0021537	telencephalon development	29	284	2.579e-02
GO:BP	GO:0019693	ribose phosphate metabolic process	36	380	2.629e-02
GO:BP	GO:0007088	regulation of mitotic nuclear division	16	121	2.631e-02
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	16	121	2.631e-02
GO:BP	GO:0006259	DNA metabolic process	78	1005	2.642e-02
GO:BP	GO:0030900	forebrain development	39	423	2.685e-02
GO:BP	GO:0010506	regulation of autophagy	35	367	2.685e-02
GO:BP	GO:0070837	dehydroascorbic acid transport	4	9	2.713e-02
GO:BP	GO:0010994	free ubiquitin chain polymerization	4	9	2.713e-02
GO:BP	GO:0006886	intracellular protein transport	57	686	2.713e-02
GO:BP	GO:0012501	programmed cell death	139	1987	2.715e-02
GO:BP	GO:0032402	melanosome transport	6	22	2.715e-02
GO:BP	GO:0010256	endomembrane system organization	52	613	2.800e-02
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	7	30	2.800e-02
GO:BP	GO:0010648	negative regulation of cell communication	105	1436	2.814e-02
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	31	314	2.820e-02
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	29	287	2.820e-02
GO:BP	GO:0000819	sister chromatid segregation	25	234	2.820e-02
GO:BP	GO:0099504	synaptic vesicle cycle	24	221	2.820e-02
GO:BP	GO:0016043	cellular component organization	493	8184	2.831e-02
GO:BP	GO:0048585	negative regulation of response to stimulus	120	1680	2.831e-02
GO:BP	GO:0048732	gland development	41	454	2.831e-02
GO:BP	GO:0001881	receptor recycling	9	48	2.836e-02
GO:BP	GO:0071363	cellular response to growth factor stimulus	57	689	2.837e-02
GO:BP	GO:0007059	chromosome segregation	39	427	2.962e-02
GO:BP	GO:0022402	cell cycle process	95	1280	2.962e-02
GO:BP	GO:0032259	methylation	25	236	3.071e-02
GO:BP	GO:0097120	receptor localization to synapse	12	79	3.077e-02
GO:BP	GO:1901135	carbohydrate derivative metabolic process	76	983	3.089e-02
GO:BP	GO:0009259	ribonucleotide metabolic process	35	372	3.098e-02
GO:BP	GO:0051904	pigment granule transport	6	23	3.234e-02
GO:BP	GO:0032401	establishment of melanosome localization	6	23	3.234e-02
GO:BP	GO:0031399	regulation of protein modification process	80	1049	3.338e-02
GO:BP	GO:0051783	regulation of nuclear division	18	149	3.338e-02
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	24	225	3.374e-02
GO:BP	GO:0043549	regulation of kinase activity	39	431	3.386e-02
GO:BP	GO:0072359	circulatory system development	86	1145	3.436e-02
GO:BP	GO:0006412	translation	59	727	3.485e-02
GO:BP	GO:0034330	cell junction organization	66	834	3.496e-02
GO:BP	GO:0032922	circadian regulation of gene expression	11	70	3.515e-02
GO:BP	GO:0050808	synapse organization	48	563	3.515e-02
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	14	103	3.567e-02
GO:BP	GO:0060395	SMAD protein signal transduction	12	81	3.634e-02
GO:BP	GO:0006643	membrane lipid metabolic process	23	214	3.691e-02
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	17	139	3.732e-02
GO:BP	GO:0033993	response to lipid	72	930	3.732e-02
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	17	139	3.732e-02
GO:BP	GO:0007346	regulation of mitotic cell cycle	43	492	3.732e-02
GO:BP	GO:0045444	fat cell differentiation	25	241	3.797e-02
GO:BP	GO:0009117	nucleotide metabolic process	43	493	3.810e-02
GO:BP	GO:0051905	establishment of pigment granule localization	6	24	3.810e-02
GO:BP	GO:0070201	regulation of establishment of protein localization	46	537	3.810e-02
GO:BP	GO:0002320	lymphoid progenitor cell differentiation	6	24	3.810e-02
GO:BP	GO:0045900	negative regulation of translational elongation	3	5	3.834e-02
GO:BP	GO:1904978	regulation of endosome organization	3	5	3.834e-02
GO:BP	GO:0009150	purine ribonucleotide metabolic process	33	351	3.892e-02
GO:BP	GO:0060998	regulation of dendritic spine development	10	61	3.915e-02
GO:BP	GO:0106027	neuron projection organization	13	94	4.213e-02
GO:BP	GO:0099003	vesicle-mediated transport in synapse	26	257	4.253e-02
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	50	600	4.253e-02
GO:BP	GO:0070848	response to growth factor	58	721	4.296e-02
GO:BP	GO:0016567	protein ubiquitination	61	768	4.441e-02
GO:BP	GO:0006915	apoptotic process	133	1923	4.441e-02
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	15	118	4.477e-02
GO:BP	GO:0051046	regulation of secretion	51	617	4.484e-02
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	31	327	4.502e-02
GO:BP	GO:0036465	synaptic vesicle recycling	13	95	4.502e-02
GO:BP	GO:0032967	positive regulation of collagen biosynthetic process	6	25	4.505e-02
GO:BP	GO:0032400	melanosome localization	6	25	4.505e-02
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	6	25	4.505e-02
GO:BP	GO:0000070	mitotic sister chromatid segregation	21	193	4.549e-02
GO:BP	GO:0070887	cellular response to chemical stimulus	149	2192	4.549e-02
GO:BP	GO:0007049	cell cycle	117	1663	4.596e-02
GO:BP	GO:0140053	mitochondrial gene expression	19	168	4.678e-02
GO:BP	GO:0060999	positive regulation of dendritic spine development	8	43	4.694e-02
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	10	63	4.716e-02
GO:BP	GO:0043488	regulation of mRNA stability	20	181	4.725e-02
GO:BP	GO:0050790	regulation of catalytic activity	71	928	4.881e-02
GO:BP	GO:0051240	positive regulation of multicellular organismal process	117	1667	4.887e-02
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	17	144	4.912e-02
GO:BP	GO:0007614	short-term memory	4	11	4.942e-02
GO:BP	GO:0016185	synaptic vesicle budding from presynaptic endocytic zone membrane	4	11	4.942e-02
GO:BP	GO:0006784	heme A biosynthetic process	4	11	4.942e-02
GO:BP	GO:0046160	heme a metabolic process	4	11	4.942e-02
GO:BP	GO:1901700	response to oxygen-containing compound	117	1669	4.974e-02
GO:BP	GO:0140694	membraneless organelle assembly	38	430	4.974e-02

#GO:BP
table_DOX24Tshare_genes_GOBP_RUV <- table_DOX24Tshare_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24Tshare_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24T Shared DEGs Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# #KEGG
# table_DOX24Tshare_genes_KEGG_RUV <- table_DOX24Tshare_genes_RUV %>% 
#   dplyr::filter(source=="KEGG") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX24Tshare_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX24T Shared DEGs Enriched KEGG Terms RUVs")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("KEGG term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))

#####DOX24R DEGs GO KEGG#####
D24R_DEGs_mat_RUV <- as.matrix(DOX24R_DEGs_GO_RUV)

DOX_24R_dxr_gene_RUV <- gost(query = D24R_DEGs_mat_RUV,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

#check if there are any KEGG terms popping up
unique(DOX_24R_dxr_gene_RUV$result$source)

[1] "GO:BP"

#only GO:BP appearing

DOX_24R_gost_genes_RUV <- 
  gostplot(DOX_24R_dxr_gene_RUV, capped = FALSE, interactive = TRUE)
DOX_24R_gost_genes_RUV

table_DOX24R_genes_RUV <- DOX_24R_dxr_gene_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX24R_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0019538	protein metabolic process	150	4721	7.286e-05
GO:BP	GO:0006796	phosphate-containing compound metabolic process	87	2407	4.484e-04
GO:BP	GO:0006793	phosphorus metabolic process	87	2410	4.484e-04
GO:BP	GO:0048731	system development	124	4053	2.938e-03
GO:BP	GO:0048518	positive regulation of biological process	176	6264	2.938e-03
GO:BP	GO:0036211	protein modification process	94	2846	2.938e-03
GO:BP	GO:0048522	positive regulation of cellular process	168	5920	2.938e-03
GO:BP	GO:0001932	regulation of protein phosphorylation	36	779	4.837e-03
GO:BP	GO:0051246	regulation of protein metabolic process	67	1855	4.837e-03
GO:BP	GO:0006629	lipid metabolic process	54	1391	4.837e-03
GO:BP	GO:0031399	regulation of protein modification process	44	1049	4.955e-03
GO:BP	GO:0080090	regulation of primary metabolic process	153	5390	5.410e-03
GO:BP	GO:0032879	regulation of localization	70	2029	8.866e-03
GO:BP	GO:0006468	protein phosphorylation	48	1227	9.315e-03
GO:BP	GO:0034311	diol metabolic process	6	31	9.494e-03
GO:BP	GO:0046173	polyol biosynthetic process	8	61	9.494e-03
GO:BP	GO:0051130	positive regulation of cellular component organization	44	1105	9.494e-03
GO:BP	GO:0046486	glycerolipid metabolic process	22	398	9.494e-03
GO:BP	GO:0042325	regulation of phosphorylation	36	830	9.494e-03
GO:BP	GO:0048519	negative regulation of biological process	161	5834	9.494e-03
GO:BP	GO:0043412	macromolecule modification	95	3030	9.494e-03
GO:BP	GO:0006950	response to stress	117	3948	9.494e-03
GO:BP	GO:0007049	cell cycle	59	1663	1.114e-02
GO:BP	GO:0007275	multicellular organism development	134	4727	1.238e-02
GO:BP	GO:0019220	regulation of phosphate metabolic process	39	956	1.238e-02
GO:BP	GO:0048513	animal organ development	95	3085	1.238e-02
GO:BP	GO:0051174	regulation of phosphorus metabolic process	39	957	1.238e-02
GO:BP	GO:0003018	vascular process in circulatory system	17	272	1.273e-02
GO:BP	GO:0032502	developmental process	175	6553	1.356e-02
GO:BP	GO:0034312	diol biosynthetic process	5	22	1.356e-02
GO:BP	GO:0016310	phosphorylation	49	1320	1.356e-02
GO:BP	GO:0042311	vasodilation	7	51	1.429e-02
GO:BP	GO:0031401	positive regulation of protein modification process	29	637	1.429e-02
GO:BP	GO:0001934	positive regulation of protein phosphorylation	24	483	1.485e-02
GO:BP	GO:0051248	negative regulation of protein metabolic process	30	677	1.608e-02
GO:BP	GO:0008654	phospholipid biosynthetic process	16	257	1.640e-02
GO:BP	GO:0033554	cellular response to stress	62	1830	1.640e-02
GO:BP	GO:0033036	macromolecule localization	97	3228	1.669e-02
GO:BP	GO:0042127	regulation of cell population proliferation	58	1685	1.726e-02
GO:BP	GO:0080134	regulation of response to stress	50	1387	1.726e-02
GO:BP	GO:0032465	regulation of cytokinesis	9	94	2.015e-02
GO:BP	GO:0035556	intracellular signal transduction	90	2965	2.015e-02
GO:BP	GO:0072359	circulatory system development	43	1145	2.031e-02
GO:BP	GO:0006259	DNA metabolic process	39	1005	2.055e-02
GO:BP	GO:0006996	organelle organization	105	3594	2.055e-02
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	15	242	2.199e-02
GO:BP	GO:0042327	positive regulation of phosphorylation	24	506	2.199e-02
GO:BP	GO:0006974	DNA damage response	36	908	2.263e-02
GO:BP	GO:0051726	regulation of cell cycle	41	1087	2.318e-02
GO:BP	GO:0051128	regulation of cellular component organization	76	2433	2.563e-02
GO:BP	GO:0043010	camera-type eye development	19	363	2.733e-02
GO:BP	GO:0045017	glycerolipid biosynthetic process	15	250	2.769e-02
GO:BP	GO:0055013	cardiac muscle cell development	8	80	2.769e-02
GO:BP	GO:0008283	cell population proliferation	65	2015	2.908e-02
GO:BP	GO:0006729	tetrahydrobiopterin biosynthetic process	3	7	2.908e-02
GO:BP	GO:0018193	peptidyl-amino acid modification	29	686	2.908e-02
GO:BP	GO:0048856	anatomical structure development	159	5997	2.947e-02
GO:BP	GO:0097009	energy homeostasis	8	83	3.155e-02
GO:BP	GO:0019637	organophosphate metabolic process	40	1077	3.155e-02
GO:BP	GO:0008610	lipid biosynthetic process	30	729	3.322e-02
GO:BP	GO:0051049	regulation of transport	54	1607	3.475e-02
GO:BP	GO:0032880	regulation of protein localization	35	907	3.532e-02
GO:BP	GO:0055006	cardiac cell development	8	86	3.577e-02
GO:BP	GO:0071881	adenylate cyclase-inhibiting adrenergic receptor signaling pathway	2	2	3.577e-02
GO:BP	GO:0060661	submandibular salivary gland formation	2	2	3.577e-02
GO:BP	GO:1905820	positive regulation of chromosome separation	5	32	3.577e-02
GO:BP	GO:0046146	tetrahydrobiopterin metabolic process	3	8	3.577e-02
GO:BP	GO:0007399	nervous system development	79	2604	3.577e-02
GO:BP	GO:0007417	central nervous system development	39	1061	3.577e-02
GO:BP	GO:0010646	regulation of cell communication	100	3486	3.577e-02
GO:BP	GO:0019751	polyol metabolic process	9	109	3.577e-02
GO:BP	GO:0023051	regulation of signaling	100	3478	3.577e-02
GO:BP	GO:0042558	pteridine-containing compound metabolic process	5	32	3.577e-02
GO:BP	GO:0022402	cell cycle process	45	1280	3.577e-02
GO:BP	GO:0045806	negative regulation of endocytosis	7	67	3.577e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	36	954	3.606e-02
GO:BP	GO:0001654	eye development	20	415	3.638e-02
GO:BP	GO:0030540	female genitalia development	4	19	3.921e-02
GO:BP	GO:0150063	visual system development	20	419	3.985e-02
GO:BP	GO:0048523	negative regulation of cellular process	149	5629	3.985e-02
GO:BP	GO:0090407	organophosphate biosynthetic process	26	619	4.255e-02
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	40	1113	4.255e-02
GO:BP	GO:0006644	phospholipid metabolic process	19	392	4.255e-02
GO:BP	GO:0010564	regulation of cell cycle process	29	720	4.255e-02
GO:BP	GO:0051924	regulation of calcium ion transport	14	244	4.255e-02
GO:BP	GO:0006281	DNA repair	26	621	4.376e-02
GO:BP	GO:0048880	sensory system development	20	426	4.449e-02
GO:BP	GO:0048583	regulation of response to stimulus	111	3993	4.449e-02
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	24	560	4.707e-02
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	24	560	4.707e-02
GO:BP	GO:0030154	cell differentiation	121	4437	4.707e-02
GO:BP	GO:0043542	endothelial cell migration	13	221	4.707e-02
GO:BP	GO:0048869	cellular developmental process	121	4438	4.707e-02
GO:BP	GO:0055007	cardiac muscle cell differentiation	9	117	4.707e-02
GO:BP	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	10	142	4.715e-02
GO:BP	GO:0050789	regulation of biological process	291	12336	4.775e-02
GO:BP	GO:0006650	glycerophospholipid metabolic process	16	309	4.824e-02
GO:BP	GO:0046165	alcohol biosynthetic process	10	143	4.825e-02
GO:BP	GO:0045859	regulation of protein kinase activity	19	402	4.874e-02
GO:BP	GO:0065007	biological regulation	299	12743	4.967e-02

#GO:BP
table_DOX24R_genes_GOBP_RUV <- table_DOX24R_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX24R_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX24R Specific DEGs Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# #KEGG
# table_DOX24R_genes_KEGG_RUV <- table_DOX24R_genes_RUV %>% 
#   dplyr::filter(source=="KEGG") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX24R_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX24R DEGs Enriched KEGG Terms RUVs")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("KEGG term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))

####DOX144R DEGs GO KEGG#####
D144R_DEGs_mat_RUV <- as.matrix(DOX144R_DEGs_GO_RUV)

DOX_144R_dxr_gene_RUV <- gost(query = D144R_DEGs_mat_RUV,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

#check if there are any KEGG terms popping up
unique(DOX_144R_dxr_gene_RUV$result$source)

[1] "GO:BP" "KEGG" 

#GO:BP and KEGG appearing here

DOX_144R_gost_genes_RUV <- 
  gostplot(DOX_144R_dxr_gene_RUV, capped = FALSE, interactive = TRUE)
DOX_144R_gost_genes_RUV

table_DOX144R_genes_RUV <- DOX_144R_dxr_gene_RUV$result %>%
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX144R_genes_RUV %>%
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>%
  kableExtra::kable(.,) %>%
  kableExtra::kable_paper("striped", full_width = FALSE) %>%
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>%
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0033058	directional locomotion	1	3	1.726e-02
GO:BP	GO:0007215	glutamate receptor signaling pathway	1	51	2.781e-02
GO:BP	GO:2000463	positive regulation of excitatory postsynaptic potential	1	33	2.781e-02
GO:BP	GO:1990806	ligand-gated ion channel signaling pathway	1	37	2.781e-02
GO:BP	GO:1903539	protein localization to postsynaptic membrane	1	55	2.781e-02
GO:BP	GO:0098976	excitatory chemical synaptic transmission	1	12	2.781e-02
GO:BP	GO:0098815	modulation of excitatory postsynaptic potential	1	50	2.781e-02
GO:BP	GO:0051968	positive regulation of synaptic transmission, glutamatergic	1	36	2.781e-02
GO:BP	GO:0050885	neuromuscular process controlling balance	1	56	2.781e-02
GO:BP	GO:0062237	protein localization to postsynapse	1	56	2.781e-02
GO:BP	GO:0048168	regulation of neuronal synaptic plasticity	1	58	2.781e-02
GO:BP	GO:0035235	ionotropic glutamate receptor signaling pathway	1	23	2.781e-02
GO:BP	GO:1902414	protein localization to cell junction	1	119	3.261e-02
GO:BP	GO:0051966	regulation of synaptic transmission, glutamatergic	1	77	3.261e-02
GO:BP	GO:0042177	negative regulation of protein catabolic process	1	117	3.261e-02
GO:BP	GO:0060079	excitatory postsynaptic potential	1	108	3.261e-02
GO:BP	GO:0060291	long-term synaptic potentiation	1	110	3.261e-02
GO:BP	GO:0035418	protein localization to synapse	1	89	3.261e-02
GO:BP	GO:0035249	synaptic transmission, glutamatergic	1	109	3.261e-02
GO:BP	GO:0099565	chemical synaptic transmission, postsynaptic	1	118	3.261e-02
GO:BP	GO:0031644	regulation of nervous system process	1	118	3.261e-02
GO:BP	GO:0060078	regulation of postsynaptic membrane potential	1	148	3.871e-02
GO:BP	GO:0050806	positive regulation of synaptic transmission	1	180	4.166e-02
GO:BP	GO:0097553	calcium ion transmembrane import into cytosol	1	181	4.166e-02
GO:BP	GO:0050905	neuromuscular process	1	175	4.166e-02
GO:BP	GO:0048167	regulation of synaptic plasticity	1	223	4.936e-02
GO:BP	GO:0019722	calcium-mediated signaling	1	234	4.987e-02
KEGG	KEGG:05031	Amphetamine addiction	1	69	3.253e-02
KEGG	KEGG:05030	Cocaine addiction	1	49	3.253e-02
KEGG	KEGG:05033	Nicotine addiction	1	40	3.253e-02
KEGG	KEGG:04720	Long-term potentiation	1	67	3.253e-02
KEGG	KEGG:04724	Glutamatergic synapse	1	115	3.615e-02
KEGG	KEGG:04713	Circadian entrainment	1	97	3.615e-02
KEGG	KEGG:05017	Spinocerebellar ataxia	1	141	3.799e-02
KEGG	KEGG:05034	Alcoholism	1	187	4.408e-02
KEGG	KEGG:04020	Calcium signaling pathway	1	251	4.646e-02
KEGG	KEGG:05020	Prion disease	1	271	4.646e-02
KEGG	KEGG:04024	cAMP signaling pathway	1	223	4.646e-02

#GO:BP
table_DOX144R_genes_GOBP_RUV <- table_DOX144R_genes_RUV %>%
  dplyr::filter(source=="GO:BP") %>%
  dplyr::select(p_value, term_name, intersection_size) %>%
  dplyr::slice_min(., n=10, order_by=p_value) %>%
  mutate(log_val = -log10(p_value))

table_DOX144R_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX144R Specific DEGs Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_DOX144R_genes_KEGG_RUV <- table_DOX144R_genes_RUV %>%
  dplyr::filter(source=="KEGG") %>%
  dplyr::select(p_value, term_name, intersection_size) %>%
  dplyr::slice_min(., n=10, order_by=p_value) %>%
  mutate(log_val = -log10(p_value))

table_DOX144R_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX144R DEGs Enriched KEGG Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####DOX144R shared DEGs GO KEGG#####
D144Rshare_DEGs_mat_RUV <- as.matrix(DOX144Rshare_DEGs_GO_plot_RUV)

DOX_144Rshare_dxr_gene_RUV <- gost(query = D144Rshare_DEGs_mat_RUV,
                      organism = "hsapiens",
                      ordered_query = FALSE,
                      measure_underrepresentation = FALSE,
                      evcodes = FALSE,
                      user_threshold = 0.05,
                      correction_method = c("fdr"),
                      sources = c("GO:BP", "KEGG"))

#check if any KEGG terms are appearing
unique(DOX_144Rshare_dxr_gene_RUV$result$source)

[1] "GO:BP"

#only GO:BP appearing here

DOX_144Rshare_gost_genes_RUV <- 
  gostplot(DOX_144Rshare_dxr_gene_RUV, capped = FALSE, interactive = TRUE)
DOX_144Rshare_gost_genes_RUV

table_DOX144Rshare_genes_RUV <- DOX_144Rshare_dxr_gene_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_DOX144Rshare_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:1903539	protein localization to postsynaptic membrane	2	55	1.412e-02
GO:BP	GO:0000278	mitotic cell cycle	4	892	1.412e-02
GO:BP	GO:0045787	positive regulation of cell cycle	3	351	1.412e-02
GO:BP	GO:1903047	mitotic cell cycle process	4	745	1.412e-02
GO:BP	GO:0051293	establishment of spindle localization	2	63	1.412e-02
GO:BP	GO:0051294	establishment of spindle orientation	2	47	1.412e-02
GO:BP	GO:0062237	protein localization to postsynapse	2	56	1.412e-02
GO:BP	GO:0090068	positive regulation of cell cycle process	3	262	1.412e-02
GO:BP	GO:0051653	spindle localization	2	68	1.463e-02
GO:BP	GO:1904860	DNA synthesis involved in mitotic DNA replication	1	1	1.598e-02
GO:BP	GO:0090592	DNA synthesis involved in DNA replication	1	1	1.598e-02
GO:BP	GO:0035418	protein localization to synapse	2	89	1.878e-02
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	2	93	1.893e-02
GO:BP	GO:0051225	spindle assembly	2	136	2.197e-02
GO:BP	GO:0046120	deoxyribonucleoside biosynthetic process	1	3	2.197e-02
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	2	114	2.197e-02
GO:BP	GO:0046126	pyrimidine deoxyribonucleoside biosynthetic process	1	3	2.197e-02
GO:BP	GO:0033058	directional locomotion	1	3	2.197e-02
GO:BP	GO:1902414	protein localization to cell junction	2	119	2.197e-02
GO:BP	GO:0110032	positive regulation of G2/MI transition of meiotic cell cycle	1	3	2.197e-02
GO:BP	GO:0046105	thymidine biosynthetic process	1	3	2.197e-02
GO:BP	GO:0022402	cell cycle process	4	1280	2.197e-02
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	2	124	2.197e-02
GO:BP	GO:0007088	regulation of mitotic nuclear division	2	121	2.197e-02
GO:BP	GO:0051296	establishment of meiotic spindle orientation	1	4	2.440e-02
GO:BP	GO:0090233	negative regulation of spindle checkpoint	1	5	2.440e-02
GO:BP	GO:0051783	regulation of nuclear division	2	149	2.440e-02
GO:BP	GO:0140499	negative regulation of mitotic spindle assembly checkpoint signaling	1	5	2.440e-02
GO:BP	GO:1901995	positive regulation of meiotic cell cycle phase transition	1	4	2.440e-02
GO:BP	GO:0046125	pyrimidine deoxyribonucleoside metabolic process	1	5	2.440e-02
GO:BP	GO:0110030	regulation of G2/MI transition of meiotic cell cycle	1	5	2.440e-02
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	2	164	2.440e-02
GO:BP	GO:0051301	cell division	3	658	2.440e-02
GO:BP	GO:0046134	pyrimidine nucleoside biosynthetic process	1	5	2.440e-02
GO:BP	GO:0046104	thymidine metabolic process	1	5	2.440e-02
GO:BP	GO:0030010	establishment of cell polarity	2	159	2.440e-02
GO:BP	GO:0010564	regulation of cell cycle process	3	720	2.458e-02
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	2	186	2.494e-02
GO:BP	GO:0007049	cell cycle	4	1663	2.494e-02
GO:BP	GO:0051661	maintenance of centrosome location	1	6	2.570e-02
GO:BP	GO:1904778	positive regulation of protein localization to cell cortex	1	6	2.570e-02
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	1	7	2.794e-02
GO:BP	GO:1901977	negative regulation of cell cycle checkpoint	1	7	2.794e-02
GO:BP	GO:0007051	spindle organization	2	206	2.794e-02
GO:BP	GO:1903046	meiotic cell cycle process	2	224	2.926e-02
GO:BP	GO:0016311	dephosphorylation	2	218	2.926e-02
GO:BP	GO:1905832	positive regulation of spindle assembly	1	8	2.926e-02
GO:BP	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	1	8	2.926e-02
GO:BP	GO:1904776	regulation of protein localization to cell cortex	1	9	3.038e-02
GO:BP	GO:0007163	establishment or maintenance of cell polarity	2	234	3.038e-02
GO:BP	GO:0062033	positive regulation of mitotic sister chromatid segregation	1	9	3.038e-02
GO:BP	GO:0051295	establishment of meiotic spindle localization	1	9	3.038e-02
GO:BP	GO:0032886	regulation of microtubule-based process	2	266	3.566e-02
GO:BP	GO:0009120	deoxyribonucleoside metabolic process	1	11	3.566e-02
GO:BP	GO:0072697	protein localization to cell cortex	1	11	3.566e-02
GO:BP	GO:0051657	maintenance of organelle location	1	12	3.569e-02
GO:BP	GO:0007056	spindle assembly involved in female meiosis	1	12	3.569e-02
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	1	12	3.569e-02
GO:BP	GO:0098976	excitatory chemical synaptic transmission	1	12	3.569e-02
GO:BP	GO:0140014	mitotic nuclear division	2	282	3.664e-02
GO:BP	GO:0051321	meiotic cell cycle	2	297	3.987e-02
GO:BP	GO:0061469	regulation of type B pancreatic cell proliferation	1	15	4.110e-02
GO:BP	GO:0044771	meiotic cell cycle phase transition	1	15	4.110e-02
GO:BP	GO:0090306	meiotic spindle assembly	1	15	4.110e-02
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	2	327	4.383e-02
GO:BP	GO:0045842	positive regulation of mitotic metaphase/anaphase transition	1	17	4.383e-02
GO:BP	GO:0051726	regulation of cell cycle	3	1087	4.383e-02
GO:BP	GO:1902969	mitotic DNA replication	1	17	4.383e-02
GO:BP	GO:0006213	pyrimidine nucleoside metabolic process	1	18	4.507e-02
GO:BP	GO:1902101	positive regulation of metaphase/anaphase transition of cell cycle	1	18	4.507e-02
GO:BP	GO:0034404	nucleobase-containing small molecule biosynthetic process	1	19	4.561e-02
GO:BP	GO:0006089	lactate metabolic process	1	19	4.561e-02
GO:BP	GO:0009163	nucleoside biosynthetic process	1	19	4.561e-02
GO:BP	GO:0033043	regulation of organelle organization	3	1148	4.614e-02
GO:BP	GO:1990778	protein localization to cell periphery	2	365	4.778e-02
GO:BP	GO:0006670	sphingosine metabolic process	1	21	4.778e-02
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	1	21	4.778e-02
GO:BP	GO:0006796	phosphate-containing compound metabolic process	4	2407	4.814e-02
GO:BP	GO:0006793	phosphorus metabolic process	4	2410	4.814e-02
GO:BP	GO:0000212	meiotic spindle organization	1	22	4.817e-02
GO:BP	GO:0046519	sphingoid metabolic process	1	23	4.912e-02
GO:BP	GO:0035235	ionotropic glutamate receptor signaling pathway	1	23	4.912e-02
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	1	24	4.944e-02
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	1	24	4.944e-02
GO:BP	GO:0009162	deoxyribonucleoside monophosphate metabolic process	1	24	4.944e-02
GO:BP	GO:1901659	glycosyl compound biosynthetic process	1	25	4.974e-02
GO:BP	GO:0090231	regulation of spindle checkpoint	1	25	4.974e-02
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	1	25	4.974e-02

#GO:BP
table_DOX144Rshare_genes_GOBP_RUV <- table_DOX144Rshare_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_DOX144Rshare_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("DOX144R Shared DEGs Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "RUVs GO KEGG-11.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# #KEGG
# table_DOX144Rshare_genes_KEGG_RUV <- table_DOX144Rshare_genes_RUV %>% 
#   dplyr::filter(source=="KEGG") %>% 
#   dplyr::select(p_value, term_name, intersection_size) %>% 
#   dplyr::slice_min(., n=10, order_by=p_value) %>% 
#   mutate(log_val = -log10(p_value))
# 
# table_DOX144Rshare_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
#   geom_point(aes(size = intersection_size)) +
#   ggtitle("DOX144R Shared DEGs Enriched KEGG Terms RUVs")+
#   xlab(expression("-log"[10]~"p-value"))+
#   guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
#   ylab("KEGG term")+
#   scale_y_discrete(labels = scales::label_wrap(30))+
#   theme_bw()+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         axis.ticks = element_line(linewidth = 1.5),
#         axis.line = element_line(linewidth = 1.5),
#         axis.text = element_text(size = 10, colour = "black", angle = 0),
#         strip.text = element_text(size = 15, colour = "black", face = "bold"))

#Plot DDR Genes logFC Heatmap RUVs k=1

#DDR Gene Expression Heatmap — DOX Over Recovery Time (68 genes, with categories)
#now add in the RUV corrected data and see if this makes a difference at all!

# Load libraries
# library(circlize)
# library(grid)
# library(reshape2)

# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T_R <- load_deg("data/new/DEGs/Toptable_RUV_24T_final.csv")
DOX_24R_R <- load_deg("data/new/DEGs/Toptable_RUV_24R_final.csv")
DOX_144R_R <- load_deg("data/new/DEGs/Toptable_RUV_144R_final.csv")

# Final Entrez IDs and categories (68 genes)
#no need to change the name of this as it's the same
entrez_category_DDR <- tribble(
  ~ENTREZID, ~Category,
  317, "Apoptosis", 355, "Apoptosis", 581, "Apoptosis", 637, "Apoptosis",
  836, "Apoptosis", 841, "Apoptosis", 842, "Apoptosis", 27113, "Apoptosis",
  5366, "Apoptosis", 54205, "Apoptosis", 55367, "Apoptosis", 8795, "Apoptosis",
  1026, "Cell Cycle / Checkpoint", 1027, "Cell Cycle / Checkpoint", 595, "Cell Cycle / Checkpoint",
  894, "Cell Cycle / Checkpoint", 896, "Cell Cycle / Checkpoint", 898, "Cell Cycle / Checkpoint",
  9133, "Cell Cycle / Checkpoint", 9134, "Cell Cycle / Checkpoint", 891, "Cell Cycle / Checkpoint",
  983, "Cell Cycle / Checkpoint", 1017, "Cell Cycle / Checkpoint", 1019, "Cell Cycle / Checkpoint",
  1020, "Cell Cycle / Checkpoint", 1021, "Cell Cycle / Checkpoint", 993, "Cell Cycle / Checkpoint",
  995, "Cell Cycle / Checkpoint", 1869, "Cell Cycle / Checkpoint", 4609, "Cell Cycle / Checkpoint",
  5925, "Cell Cycle / Checkpoint", 9874, "Cell Cycle / Checkpoint", 11011, "Cell Cycle / Checkpoint",
  1385, "Cell Cycle / Checkpoint",
  472, "Damage Sensors / Signal Transducers", 545, "Damage Sensors / Signal Transducers",
  5591, "Damage Sensors / Signal Transducers", 5810, "Damage Sensors / Signal Transducers",
  5883, "Damage Sensors / Signal Transducers", 5884, "Damage Sensors / Signal Transducers",
  6118, "Damage Sensors / Signal Transducers", 4361, "Damage Sensors / Signal Transducers",
  10111, "Damage Sensors / Signal Transducers", 4683, "Damage Sensors / Signal Transducers",
  84126, "Damage Sensors / Signal Transducers", 3014, "Damage Sensors / Signal Transducers",
  672, "DNA Repair", 2177, "DNA Repair", 5888, "DNA Repair", 5893, "DNA Repair",
  1647, "DNA Repair", 4616, "DNA Repair", 10912, "DNA Repair", 1111, "DNA Repair",
  11200, "DNA Repair", 1643, "DNA Repair", 8243, "DNA Repair", 5981, "DNA Repair",
  7157, "p53 Regulators / Targets", 4193, "p53 Regulators / Targets", 5371, "p53 Regulators / Targets",
  27244, "p53 Regulators / Targets", 50484, "p53 Regulators / Targets",
  207, "Miscellaneous / Broad", 25, "Miscellaneous / Broad"
)

entrez_ids_DDR_R <- entrez_category_DDR$ENTREZID

# saveRDS(entrez_ids_DDR_R, "data/new/RUV/DDR_genes_entrezid.RDS")

# Extract relevant DEG values
extract_data_DDR_R <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_DDR_R) %>%
    mutate(
      Gene = mapIds(org.Hs.eg.db, as.character(Entrez_ID),
                    column = "SYMBOL", keytype = "ENTREZID", multiVals = "first"),
      Condition = name,
      Signif = ifelse(adj.P.Val < 0.05, "*", "")
    )
}

# DEG list
deg_list_RUV <- list("DOX_24T" = DOX_24T_R, 
                 "DOX_24R" = DOX_24R_R, 
                 "DOX_144R" = DOX_144R_R
)

# Combine all DEGs and annotate
all_data_DDR_RUV <- bind_rows(mapply(extract_data_DDR_R, deg_list_RUV, names(deg_list_RUV), SIMPLIFY = FALSE)) %>%
  left_join(entrez_category_DDR, by = c("Entrez_ID" = "ENTREZID"))

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

# DDR_genesymbols_list_RUV <- all_data_DDR_RUV$Gene
# write.csv(DDR_genesymbols_list_RUV, "data/new/RUV/DDR_Genes_list_RUV.csv")

# Create matrices
logFC_matddr_R <- acast(all_data_DDR_RUV, Gene ~ Condition, value.var = "logFC")
signif_matddr_R <- acast(all_data_DDR_RUV, Gene ~ Condition, value.var = "Signif")

# Set desired order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_DDR_RUV <- logFC_matddr_R[, desired_order, drop = FALSE]
signif_mat_DDR_RUV <- signif_matddr_R[, desired_order, drop = FALSE]

# Column annotation
meta_DDR_R <- str_split_fixed(colnames(logFC_mat_DDR_RUV), "_", 2)
col_annot <- HeatmapAnnotation(
  Drug = meta_DDR_R[, 1],
  Time = meta_DDR_R[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(1, 1, 1), "cm")
)

# Row annotation
gene_order_df_DDR_RUV <- all_data_DDR_RUV %>%
  distinct(Gene, Category) %>%
  arrange(factor(Category, levels = sort(unique(entrez_category_DDR$Category))), Gene)

ordered_genes_DDR_RUV <- gene_order_df_DDR_RUV$Gene
logFC_mat_DDR_RUV <- logFC_mat_DDR_RUV[ordered_genes_DDR_RUV, ]
signif_mat_DDR_RUV <- signif_mat_DDR_RUV[ordered_genes_DDR_RUV, ]

category_colors_DDR <- structure(
  c("darkorange", "steelblue", "darkgreen", "firebrick", "mediumpurple", "gray60"),
  names = sort(unique(entrez_category_DDR$Category))
)

ha_left_DDR_RUV <- rowAnnotation(
  Category = gene_order_df_DDR_RUV$Category,
  col = list(Category = category_colors_DDR),
  annotation_name_side = "top"
)

# Final Heatmap
Heatmap(logFC_mat_DDR_RUV,
        name = "logFC",
        top_annotation = col_annot,
        left_annotation = ha_left_DDR_RUV,
        cluster_columns = FALSE,
        cluster_rows = FALSE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        row_names_gp = gpar(fontsize = 10),
        column_title = "DDR Gene Expression Response (n = 68)\n DOX Recovery (RUVs Corrected)",
        column_title_gp = gpar(fontsize = 14, fontface = "bold"),
        cell_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_DDR[i, j], x, y, gp = gpar(fontsize = 9))
        }
)

Past versions of "RUVs DDR Genes logFC-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08
0b1ffad	emmapfort	2025-07-02

##LogFC of DDR Gene Set after RUVs Correction

library(car)

Loading required package: carData

Attaching package: 'car'

The following object is masked from 'package:VennDiagram':

    ellipse

The following object is masked from 'package:dplyr':

    recode

The following object is masked from 'package:purrr':

    some

#get an overall idea of the response occurring in all genes with logFC across time
#start with the logFC and then do the abs logFC

####data setup####
#Read DNA Damage Response Gene List

#this had an extra column that was unncessesary
# DNA_damage <- read.csv("data/new/RUV/DDR_Genes_list_RUV.csv", stringsAsFactors = FALSE) %>% 
#   dplyr::select(-(X))
#   
# names(DNA_damage)[names(DNA_damage) == "x"] <- "Symbol"
#   
#saveRDS(DNA_damage, "data/new/RUV/DNA_damage_genesymbols.RDS")

#this is the final processed version with a single list of symbols with col name
DNA_damage <- readRDS("data/new/RUV/DNA_damage_genesymbols.RDS")

#Convert gene symbols to Entrez IDs
DNA_damage <- DNA_damage %>%
  mutate(Entrez_ID = mapIds(org.Hs.eg.db,
                            keys = Symbol,
                            column = "ENTREZID",
                            keytype = "SYMBOL",
                            multiVals = "first"))

'select()' returned 1:1 mapping between keys and columns

DNA_damage_genes <- na.omit(DNA_damage$Entrez_ID)

time_colors <- c("24T" = "#238B45",
                 "24R" = "#74C476",
                 "144R" = "#C7E9C0")

#load in my DEGs which I'll use to create a combined toptable
load_deg <- function(path) read.csv(path)

DOX_24T_R <- load_deg("data/new/DEGs/Toptable_RUV_24T_final.csv")
DOX_24R_R <- load_deg("data/new/DEGs/Toptable_RUV_24R_final.csv")
DOX_144R_R <- load_deg("data/new/DEGs/Toptable_RUV_144R_final.csv")

all_toptables_RUV <- bind_rows(
  DOX_24T_R %>% mutate(Drug = "DOX", Timepoint = "24T"),
  DOX_24R_R %>% mutate(Drug = "DOX", Timepoint = "24R"),
  DOX_144R_R %>% mutate(Drug = "DOX", Timepoint = "144R"),
)


filtered_toptables_RUV <- all_toptables_RUV %>%
  filter(Entrez_ID %in% DNA_damage_genes)

filtered_toptables_RUV <- filtered_toptables_RUV %>%
  mutate(
    Drug = factor(Drug, levels = c("DOX")),
    Timepoint = factor(Timepoint, levels = c("24T", "24R", "144R"), 
                       labels = c("Timepoint: 24T", "Timepoint: 24R", "Timepoint: 144R"))
  )

levene_results_RUV <- filtered_toptables_RUV %>%
  group_by(Timepoint) %>%
  summarise(p_value = leveneTest(logFC ~ Timepoint, data = .)$`Pr(>F)`[1], .groups = "drop") %>%
  mutate(significance = ifelse(p_value < 0.05, "*", ""))  # Use p < 0.05 threshold for stars

# **🔹 Determine Y-axis position for Stars**
star_positions <- filtered_toptables_RUV %>%
  group_by(Timepoint,Drug) %>%
  summarise(y_pos = max(logFC, na.rm = TRUE) + 0.5, .groups = "drop") %>%
  group_by(Timepoint) %>%
  summarise(y_pos = max(y_pos), .groups = "drop")

# **🔹 Merge Levene test results with Y positions**
levene_results_plot_RUV <- levene_results_RUV %>%
  left_join(star_positions, by = c("Timepoint")) %>%
  mutate(x_position = 1.5)

ggplot(filtered_toptables_RUV, aes(x = Drug, y = logFC, fill = Timepoint)) +
  geom_violin(trim = FALSE, alpha = 0.5) +  # Violin plot for logFC
  geom_boxplot(width = 0.1, outlier.shape = NA, color = "black", alpha = 0.5) +  # Add boxplot inside violin
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_grid(Drug ~ Timepoint) +  
  geom_text(
    data = levene_results_plot_RUV %>% filter(significance == "*"),  # Only plot significant comparisons
    aes(x = x_position, y = y_pos, label = significance), 
    size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  ) +
  theme_bw() +
  xlab("") +
  ylab("Log Fold Change") +  
  ggtitle("LogFC Distribution for DDR Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC DDR Boxplots RUVs Genes-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# Read DNA Damage Genes List
# DNA_damage
# 
# # Convert gene symbols to Entrez IDs
# DNA_damage <- DNA_damage %>%
#   mutate(Entrez_ID = mapIds(org.Hs.eg.db,
#                             keys = Symbol,
#                             column = "ENTREZID",
#                             keytype = "SYMBOL",
#                             multiVals = "first"))
# 
# # Extract DNA damage gene Entrez IDs
# DNA_damage_genes <- na.omit(DNA_damage$Entrez_ID)
# total_DNA_damage_genes <- length(DNA_damage_genes)  # Total number of DNA damage genes
# 
# # Define DEG lists (with significant ones only)
# DOX_DEGs <- list(
#   "DOX_24T" = DEG1_RUV, "DOX_24R" = DEG2_RUV, "DOX_144R" = DEG3_RUV
# )
# 
# # Function to calculate the presence of DNA damage genes in DEGs 
# calculate_proportion_DDR <- function(deg_list, drug_name) {
#   data.frame(
#     Sample = names(deg_list),
#     Drug = drug_name,
#     DNA_Damage_DEGs = sapply(deg_list, function(ids) sum(ids %in% DNA_damage_genes)),  # DEGs present in DNA damage set
#     Non_DNA_Damage_DEGs = sapply(deg_list, function(ids) total_DNA_damage_genes - sum(ids %in% DNA_damage_genes))  # Remaining DNA damage genes
#   ) %>%
#     mutate(
#       Yes_Proportion = (DNA_Damage_DEGs / total_DNA_damage_genes) * 100,  # Percentage of DEGs in DNA damage genes
#       No_Proportion = (Non_DNA_Damage_DEGs / total_DNA_damage_genes) * 100  # Remaining DNA damage genes as No
#     )
# }
# 
# # Calculate proportions for CX-5461 and DOX
# DOX_proportion <- calculate_proportion_DDR(DOX_DEGs, "DOX")
# 
# # Convert to long format for stacked bar plot
# proportion_long <- DOX_proportion %>%
#   dplyr::select(Sample, Drug, Yes_Proportion, No_Proportion) %>%
#   pivot_longer(cols = c(Yes_Proportion, No_Proportion), names_to = "Category", values_to = "Percentage") %>%
#   mutate(Category = ifelse(Category == "Yes_Proportion", "Yes", "No"))
# 
# # **Ensure correct order of samples on X-axis**
# sample_order <- c(
#   "DOX_24T", "DOX_24R", "DOX_144R"
# )
# proportion_long$Sample <- factor(proportion_long$Sample, levels = sample_order, ordered = TRUE)
# 
# # **Fix: Ensure "Yes" is on top and "No" is at the bottom in stacked bars**
# proportion_long$Category <- factor(proportion_long$Category, levels = c("Yes", "No"))  # Ensures "Yes" on top, "No" at bottom
# 
# # **Perform Chi-Square Test for DOX across timepoints**
# chi_square_results <- data.frame(Sample = character(), P_Value = numeric())
# 
# for (i in seq(1, 6)) {  #comparing across timepoints
#   tx24_sample <- sample_order[i] #DOX24T
#   rec24_sample <- sample_order[i + 6]   #DOX24R
#   rec144_sample <- sample_order[i + 12] #DOX144R
#   
#   tx24_data <- filter(DOX_proportion, Sample == tx24_sample)
#   rec24_data <- filter(DOX_proportion, Sample == rec24_sample)
#   rec144_data <- filter(DOX_proportion, Sample == rec144_sample)
#   
#   # Construct contingency table for Chi-Square test
#   contingency_table <- matrix(
#     c(tx24_data$DNA_Damage_DEGs, tx24_data$Non_DNA_Damage_DEGs,
#       rec24_data$DNA_Damage_DEGs, rec24_data$Non_DNA_Damage_DEGs,
#       rec144_data$DNA_Damage_DEGs, rec144_data$Non_DNA_Damage_DEGs),
#     nrow = 3, byrow = TRUE
#   )
#   
#   # Run Chi-Square Test
#   test_result <- chisq.test(contingency_table)
#   p_value <- test_result$p.value
#   
#   # Store results
#   chi_square_results <- rbind(chi_square_results, data.frame(Sample = tx24_sample, P_Value = p_value))
# }
# 
# # Add significance stars
# chi_square_results$Significant <- ifelse(chi_square_results$P_Value < 0.05, "*", "")
# 
# # Merge Chi-Square results
# proportion_long <- left_join(proportion_long, chi_square_results, by = "Sample")
# 
# # **Save output**
# write.csv(proportion_long, "C:/Work/Postdoc_UTMB/CX-5461 Project/Transcriptome literatures/lit2/Proportion_Stacked_DNA_Damage_DEGs_with_ChiSquare.csv", row.names = FALSE)
# 
# 
# # Define correct factor orders for samples
# sample_order <- c(
#   "CX_0.1_3", "CX_0.1_24", "CX_0.1_48", "CX_0.5_3", "CX_0.5_24", "CX_0.5_48",
#   "DOX_0.1_3", "DOX_0.1_24", "DOX_0.1_48", "DOX_0.5_3", "DOX_0.5_24", "DOX_0.5_48"
# )
# 
# # Reapply factor levels for correct order in both proportion_data and proportion_long
# proportion_data$Sample <- factor(proportion_data$Sample, levels = sample_order, ordered = TRUE)
# proportion_long$Sample <- factor(proportion_long$Sample, levels = sample_order, ordered = TRUE)
# 
# # **Fix: Ensure "Yes" is on top and "No" is at the bottom in stacked bars**
# proportion_long$Category <- factor(proportion_long$Category, levels = c("Yes", "No")

##LogFC of DDR Genes Across Timepoints RUVs

library(rstatix)

Attaching package: 'rstatix'

The following object is masked from 'package:AnnotationDbi':

    select

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:biomaRt':

    select

The following object is masked from 'package:stats':

    filter

# Read DNA Damage Response Gene List
# DNA_damage as above

# Convert gene symbols to Entrez IDs
# DNA_damage <- DNA_damage %>%
#   mutate(Entrez_ID = mapIds(org.Hs.eg.db,
#                             keys = Symbol,
#                             column = "ENTREZID",
#                             keytype = "SYMBOL",
#                             multiVals = "first"))

# DNA_damage_genes <- na.omit(DNA_damage$Entrez_ID)

# saveRDS(DNA_damage_genes, "data/new/RUV/DNA_damage_genes_symbolentrez.RDS")

DNA_damage_genes <- readRDS("data/new/RUV/DNA_damage_genes_symbolentrez.RDS")

all_toptables_RUV <- bind_rows(
  DOX_24T_R %>% mutate(Drug = "DOX", Timepoint = "24T"),
  DOX_24R_R %>% mutate(Drug = "DOX", Timepoint = "24R"),
  DOX_144R_R %>% mutate(Drug = "DOX", Timepoint = "144R"),
)

filtered_toptables_RUV <- all_toptables_RUV %>%
  filter(Entrez_ID %in% DNA_damage_genes) %>%
  mutate(abs_logFC = abs(logFC))

filtered_toptables_RUV <- filtered_toptables_RUV %>%
  mutate(
    Drug = factor(Drug, levels = c("DOX")),
    Timepoint = factor(Timepoint, levels = c("24T", "24R", "144R"), 
                       labels = c("Timepoint: 24T", "Timepoint: 24R", "Timepoint: 144R"))
  )

wilcox_results <- filtered_toptables_RUV %>%
  wilcox_test(abs_logFC ~ Timepoint) %>%
  adjust_pvalue(method = "bonferroni") %>%
  mutate(significance = ifelse(p < 0.05, "*", ""))

#make a little thing of your timepoint comparisons
pairs <- wilcox_results %>% 
  dplyr::select(group1, group2) %>% 
  distinct()

max_per_timepoint <- filtered_toptables_RUV %>% 
  group_by(Timepoint) %>% 
  summarise(max_logFC = max(abs_logFC, na.rm = TRUE), .groups = "drop")
  
#Join max values for group1
star_positions <- pairs %>%
  left_join(max_per_timepoint, by = c("group1" = "Timepoint"))
names(star_positions)[names(star_positions) == "max_logFC"] <- "max1"

#Join max values for group2, with suffixes to avoid name conflict
star_positions <- star_positions %>%
  left_join(max_per_timepoint, by = c("group2" = "Timepoint"), suffix = c(".group1", ".group2"))
names(star_positions)[names(star_positions) == "max_logFC"] <- "max2"

star_positions <- star_positions %>% 
  mutate(y_pos = pmax(max1, max2, na.rm = TRUE) + 0.2)

#now star positions has the same group1 and group2 as wilcoxon

wilcox_results_plot <- wilcox_results %>%
  left_join(star_positions, by = c("group1", "group2")) %>%
  mutate(x_position = 1.5)  

wilcox_results_plot <- wilcox_results_plot %>% 
  mutate(group1 = gsub("Timepoint: ", "", group1),
         group2 = gsub("Timepoint: ", "", group2))

wilcox_results_plot <- wilcox_results_plot %>%
  mutate(x_position = case_when(
    group1 == "24T" & group2 == "24R" ~ 1.5,
    group1 == "24T" & group2 == "144R" ~ 2,
    group1 == "24R" & group2 == "144R" ~ 2.5
  ))

####logFC####
ggplot(filtered_toptables_RUV, aes(x = Timepoint, y = logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  geom_text(
    data = wilcox_results_plot, 
    aes(x = x_position, y = y_pos, label = significance), 
    size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  ) +
  theme_bw() +
  xlab("") +
  ylab("Log Fold Change") +  
  ggtitle("Log Fold Change for DDR Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC DDR Genes RUVs Across Timepoints-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####abs logFC####
ggplot(filtered_toptables_RUV, aes(x = Timepoint, y = abs_logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  geom_text(
    data = wilcox_results_plot, 
    aes(x = x_position, y = y_pos, label = significance), 
    size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  ) +
  theme_bw() +
  xlab("") +
  ylab("|Log Fold Change|") +  
  ggtitle("|Log Fold Change| for DDR Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC DDR Genes RUVs Across Timepoints-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#DIC Genes RUVs Corrected

#plot a list of 29 functionally validated DIC genes
# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T_R <- load_deg("data/new/DEGs/Toptable_RUV_24T_final.csv")
DOX_24R_R <- load_deg("data/new/DEGs/Toptable_RUV_24R_final.csv")
DOX_144R_R <- load_deg("data/new/DEGs/Toptable_RUV_144R_final.csv")

#the data I have is in hgnc_symbols, I want to convert this to entrez_id like my df
DIC_genes <- tribble(
  ~SYMBOL, ~Category,
  "CAT", "ROS Generation / Handling",
  "CBR1", "ROS Generation / Handling",
  "CBR3", "ROS Generation / Handling",
  "ERBB2", "ROS Generation / Handling",
  "GPX3", "ROS Generation / Handling",
  "GSTM1", "ROS Generation / Handling",
  "GSTP", "ROS Generation / Handling",
  "HAS3", "ROS Generation / Handling",
  "NOS3", "ROS Generation / Handling",
  "PLCE1", "ROS Generation / Handling",
  "RAC2", "ROS Generation / Handling",
  "SPG7", "ROS Generation / Handling",
  "PRDM2", "DNA Damage", 
  "MLH1", "DNA Damage",
  "RARG", "DNA Damage",
  "HFE", "Iron Uptake & Homeostasis",
  "SLC22A17", "DOX Uptake",
  "SLC28A1", "DOX Uptake",
  "SLC28A3", "DOX Uptake",
  "ABCB4", "DOX Efflux",
  "ABCC2", "DOX Efflux",
  "ABCC5", "DOX Efflux", 
  "ABCC9", "DOX Efflux",
  "ABCC10", "DOX Efflux",
  "CELF4", "Calcium Handling",
  "MYH7", "Calcium Handling",
  "CYP2J2", "Cardiac Electrical Activity",
  "RIN3", "Cardiac Electrical Activity",
  "ZFN521", "Cardiac Electrical Activity")

gene_df_DIC_RUV <- tibble(HGNC = DIC_genes)

gene_df_DIC_RUV <- gene_df_DIC_RUV %>% 
  mutate(Entrez_ID = mapIds(org.Hs.eg.db,
                            keys = DIC_genes$SYMBOL,
                            column = "ENTREZID", 
                            keytype = "SYMBOL", 
                            multiVals = "first")) %>% 
  unnest_wider(HGNC) %>% 
  mutate(Entrez_ID = as.character(Entrez_ID))

'select()' returned 1:1 mapping between keys and columns

# DIC_genes_symb <- gene_df_DIC_RUV %>% 
#   dplyr::select("SYMBOL", "Entrez_ID")
# saveRDS(DIC_genes_symb, "data/new/RUV/DIC_genelist_symbolentrez_RUV.RDS")

#now I've put together a dataframe with the HGNC, Category, and Entrez_ID
#plus I've ensured that Entrez_ID is a character for later joining

entrez_ids_DIC_RUV <- gene_df_DIC_RUV$Entrez_ID

# Extract relevant DEG values
extract_data_DIC_RUV <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_DIC_RUV) %>%
    mutate(
      Gene = mapIds(org.Hs.eg.db, as.character(Entrez_ID),
                    column = "SYMBOL", keytype = "ENTREZID", multiVals = "first"),
      Condition = name,
      Signif = ifelse(adj.P.Val < 0.05, "*", "")
    )
}

# DEG list
deg_list_RUV <- list("DOX_24T" = DOX_24T_R, 
                 "DOX_24R" = DOX_24R_R, 
                 "DOX_144R" = DOX_144R_R
)

# Combine all DEGs and annotate
all_data_DIC_RUV <- bind_rows(mapply(extract_data_DIC_RUV, 
                             deg_list_RUV, 
                             names(deg_list_RUV), 
                             SIMPLIFY = FALSE)) %>%
  mutate(Entrez_ID = as.character(Entrez_ID)) %>% 
  left_join(gene_df_DIC_RUV, 
            by = "Entrez_ID")

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

#I've also made sure here that Entrez_ID is a character and not an integer

# Create matrices
logFC_matdic_RUV <- acast(all_data_DIC_RUV, Gene ~ Condition, value.var = "logFC")
signif_matdic_RUV <- acast(all_data_DIC_RUV, Gene ~ Condition, value.var = "Signif")

# Set desired order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_DIC_RUV <- logFC_matdic_RUV[, desired_order, drop = FALSE]
signif_mat_DIC_RUV <- signif_matdic_RUV[, desired_order, drop = FALSE]

# Column annotation
meta_DIC_R <- str_split_fixed(colnames(logFC_mat_DIC_RUV), "_", 3)
meta_DIC_R <- str_split_fixed(colnames(logFC_mat_DIC_RUV), "_", 2)
col_annot_RUV <- HeatmapAnnotation(
  Drug = meta_DIC_R[, 1],
  Time = meta_DIC_R[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(2, 2, 2), "cm")
)
#for this I can leave off the DMSO as it's already from a pairwise comparison

#make an extra object with my category order as well
category_order_DIC <- c(
  "ROS Generation / Handling",
  "DNA Damage",
  "Calcium Handling",
  "DOX Uptake",
  "Iron Uptake & Homeostasis",
  "DOX Efflux",
  "Cardiac Electrical Activity"
)

# Row annotation
gene_order_df_DIC_RUV <- all_data_DIC_RUV %>%
  distinct(Gene, Category) %>%
  mutate(Category = factor(Category, levels = category_order_DIC)) %>% 
  arrange(Category, Gene)

ordered_genes_DIC_RUV <- gene_order_df_DIC_RUV$Gene
logFC_mat_DIC_RUV <- logFC_mat_DIC_RUV[ordered_genes_DIC_RUV, ]
signif_mat_DIC_RUV <- signif_mat_DIC_RUV[ordered_genes_DIC_RUV, ]

#add in your colors for each category
 category_colors_DIC <- structure(
  c("darkorange", "steelblue", "darkgreen", "firebrick", "gold", "mediumpurple", "gray60"),
  names = category_order_DIC
)

ha_left_DIC_RUV <- rowAnnotation(
  Category = gene_order_df_DIC_RUV$Category,
  col = list(Category = category_colors_DIC),
  annotation_name_side = "top"
)

# Draw heatmap
Heatmap(logFC_mat_DIC_RUV,
        name = "logFC",
        top_annotation = col_annot,
        left_annotation = ha_left_DIC_RUV,
        cluster_columns = FALSE,
        cluster_rows = FALSE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        cell_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_DIC[i, j], x, y, gp = gpar(fontsize = 9))
        },
        column_title = "DIC Genes Expression (n=29)\nDOX Recovery (RUVs Corrected)",
        column_title_gp = gpar(fontsize = 14, fontface = "bold")
)

Past versions of "RUVs DIC Genes logFC HM-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#get an overall idea of the logFC of these genes over timepoints
library(rstatix)
# Read DIC gene list - named DOX_cardiotox

# DOX_cardiotox <- readRDS("data/new/RUV/DIC_genelist_symbolentrez_RUV.RDS")
# 
# # Convert gene symbols to Entrez IDs
# DOX_cardiotox <- DOX_cardiotox %>%
#   mutate(Entrez_ID = mapIds(org.Hs.eg.db,
#                             keys = SYMBOL,
#                             column = "ENTREZID",
#                             keytype = "SYMBOL",
#                             multiVals = "first"))
# 
# DOX_cardiotox_genes <- na.omit(DOX_cardiotox$Entrez_ID)

# saveRDS(DOX_cardiotox_genes, "data/new/RUV/DIC_genes_symbolentrez.RDS")
#this already has both SYMBOL and Entrez_ID

DOX_cardiotox_genes <- readRDS("data/new/RUV/DIC_genes_symbolentrez.RDS")

all_toptables_RUV <- bind_rows(
  DOX_24T_R %>% mutate(Drug = "DOX", Timepoint = "24T"),
  DOX_24R_R %>% mutate(Drug = "DOX", Timepoint = "24R"),
  DOX_144R_R %>% mutate(Drug = "DOX", Timepoint = "144R"),
)

filtered_toptables_RUV_DIC <- all_toptables_RUV %>%
  filter(Entrez_ID %in% DOX_cardiotox_genes) %>%
  mutate(abs_logFC = abs(logFC))

filtered_toptables_RUV_DIC <- filtered_toptables_RUV_DIC %>%
  mutate(
    Drug = factor(Drug, levels = c("DOX")),
    Timepoint = factor(Timepoint, levels = c("24T", "24R", "144R"), 
                       labels = c("Timepoint: 24T", "Timepoint: 24R", "Timepoint: 144R"))
  )

wilcox_results_DIC <- filtered_toptables_RUV_DIC %>%
  wilcox_test(abs_logFC ~ Timepoint) %>%
  adjust_pvalue(method = "bonferroni") %>%
  mutate(significance = ifelse(p < 0.05, "*", ""))

#make a little thing of your timepoint comparisons
pairs_DIC <- wilcox_results_DIC %>% 
  dplyr::select(group1, group2) %>% 
  distinct()

max_per_timepoint_DIC <- filtered_toptables_RUV_DIC %>% 
  group_by(Timepoint) %>% 
  summarise(max_logFC = max(abs_logFC, na.rm = TRUE), .groups = "drop")
  
#Join max values for group1
star_positions_DIC <- pairs_DIC %>%
  left_join(max_per_timepoint_DIC, by = c("group1" = "Timepoint"))
names(star_positions_DIC)[names(star_positions_DIC) == "max_logFC"] <- "max1"

#Join max values for group2, with suffixes to avoid name conflict
star_positions_DIC <- star_positions_DIC %>%
  left_join(max_per_timepoint_DIC, by = c("group2" = "Timepoint"), suffix = c(".group1", ".group2"))
names(star_positions_DIC)[names(star_positions_DIC) == "max_logFC"] <- "max2"

star_positions_DIC <- star_positions_DIC %>% 
  mutate(y_pos = pmax(max1, max2, na.rm = TRUE) + 0.2)

#now star positions has the same group1 and group2 as wilcoxon

wilcox_results_plot_DIC <- wilcox_results_DIC %>%
  left_join(star_positions_DIC, by = c("group1", "group2")) %>%
  mutate(x_position = 1.5)  

wilcox_results_plot_DIC <- wilcox_results_plot_DIC %>% 
  mutate(group1 = gsub("Timepoint: ", "", group1),
         group2 = gsub("Timepoint: ", "", group2))

wilcox_results_plot_DIC <- wilcox_results_plot_DIC %>%
  mutate(x_position = case_when(
    group1 == "24T" & group2 == "24R" ~ 1.5,
    group1 == "24T" & group2 == "144R" ~ 2,
    group1 == "24R" & group2 == "144R" ~ 2.5
  ))

####logFC####
ggplot(filtered_toptables_RUV_DIC, aes(x = Timepoint, y = logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  geom_text(
    data = wilcox_results_plot_DIC, 
    aes(x = x_position, y = y_pos, label = significance), 
    size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  ) +
  theme_bw() +
  xlab("") +
  ylab("Log Fold Change") +  
  ggtitle("Log Fold Change for DIC Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC Boxplots DIC RUVs Genes-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

####abs logFC####
ggplot(filtered_toptables_RUV_DIC, aes(x = Timepoint, y = abs_logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  geom_text(
    data = wilcox_results_plot_DIC, 
    aes(x = x_position, y = y_pos, label = significance), 
    size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  ) +
  theme_bw() +
  xlab("") +
  ylab("|Log Fold Change|") +  
  ggtitle("|Log Fold Change| for DIC Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC Boxplots DIC RUVs Genes-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#p53 Target Genes logFC Heatmap RUVs Corrected

# Load libraries

# Load DEG files
load_deg <- function(path) read.csv(path)

DOX_24T_R <- load_deg("data/new/DEGs/Toptable_RUV_24T_final.csv")
DOX_24R_R <- load_deg("data/new/DEGs/Toptable_RUV_24R_final.csv")
DOX_144R_R <- load_deg("data/new/DEGs/Toptable_RUV_144R_final.csv")


#P53 target Entrez_ID
entrez_ids_p53 <- c(1026,50484,4193,9766,9518,7832,1643,1647,1263,57103,51065,8795,51499,64393,581,
                5228,5429,8493,55959,7508,64782,282991,355,53836,4814,10769,9050,27244,9540,94241,
                26154,57763,900,26999,55332,26263,23479,23612,29950,9618,10346,8824,134147,55294,
                22824,4254,6560,467,27113,60492,8444,60401,1969,220965,2232,3976,55191,84284,93129,
                5564,7803,83667,7779,132671,7039,51768,137695,93134,7633,10973,340485,307,27350,
                23245,3732,29965,1363,1435,196513,8507,8061,2517,51278,53354,54858,23228,5366,5912,
                6236,51222,26152,59,1907,50650,91012,780,9249,11072,144455,64787,116151,27165,2876,
                57822,55733,57722,121457,375449,85377,4851,5875,127544,29901,84958,8797,8793,441631,
                220001,54541,5889,5054,25816,25987,5111,98,317,598,604,10904,1294,80315,53944,
                1606,2770,3628,3675,3985,4035,4163,84552,29085,55367,5371,5791,54884,5980,8794,
                1462,50808,220,583,694,1056,9076,10978,54677,1612,55040,114907,2274,127707,4000,
                8079,4646,4747,27445,5143,80055,79156,5360,5364,23654,5565,5613,5625,10076,56963,
                6004,390,255488,6326,6330,23513,7869,283130,204962,83959,6548,6774,9263,10228,
                22954,10475,85363,494514,10142,79714,1006,8446,9648,79828,5507,55240,63874,25841,
                9289,84883,154810,51321,421,8553,655,119032,84280,10950,824,839,57828,857,8812,
                8837,94027,113189,22837,132864,10898,3300,81704,1847,1849,1947,9538,24139,5168,
                147965,115548,9873,23768,2632,2817,3280,3265,23308,3490,51477,182,3856,8844,144811,
                9404,4043,9848,2872,23041,740,343263,4638,26509,4792,22861,57523,55214,80025,164091,
                57060,64065,51090,5453,8496,333926,55671,5900,55544,23179,8601,389,6223,55800,6385,
                4088,6643,122809,257397,285343,7011,54790,374618,55362,51754,7157,9537,22906,7205,
                80705,219699,55245,83719,7748,25946,118738)

# saveRDS(entrez_ids_p53, "data/new/RUV/p53_targetgenes_entrezid.RDS")

# Function to extract relevant data
extract_data_p53_RUV <- function(df, name) {
  df %>%
    filter(Entrez_ID %in% entrez_ids_p53) %>%
    mutate(Gene = mapIds(org.Hs.eg.db, 
                         as.character(Entrez_ID),
                         column = "SYMBOL", 
                         keytype = "ENTREZID", 
                         multiVals = "first"),
           Condition = name,
           Signif = ifelse(adj.P.Val < 0.05, "*", ""))
}


# Collect all data
# DEG list
deg_list_RUV <- list("DOX_24T" = DOX_24T_R, 
                 "DOX_24R" = DOX_24R_R, 
                 "DOX_144R" = DOX_144R_R
)

# Combine all DEGs and annotate
all_data_p53_RUV <- bind_rows(mapply(extract_data_p53_RUV, deg_list_RUV, names(deg_list_RUV), SIMPLIFY = FALSE)) 

'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

#unnecessary to join again as there are not categories on this list of entrezids
# %>%
#   left_join(entrez_ids, by = c("Entrez_ID" = "ENTREZID"))

#make a list of these genes for later analysis
# saveRDS(all_data_p53_RUV, "data/new/RUV/p53_targetgenes_RUV.RDS")

# p53_genes <- all_data_p53_RUV %>% 
#   dplyr::select("SYMBOL", "Entrez_ID")

# saveRDS(p53_genes, "data/new/RUV/p53_genes_symbolentrez.RDS")

# Create matrices
logFC_mat53_RUV <- acast(all_data_p53_RUV, Gene ~ Condition, value.var = "logFC")
signif_mat53_RUV <- acast(all_data_p53_RUV, Gene ~ Condition, value.var = "Signif")

# Desired column order
desired_order <- c("DOX_24T",
                   "DOX_24R",
                   "DOX_144R")

logFC_mat_p53_RUV <- logFC_mat53_RUV[, desired_order]
signif_mat_p53_RUV <- signif_mat53_RUV[, desired_order]

# Column annotation
meta_p53_RUV <- str_split_fixed(colnames(logFC_mat_p53_RUV), "_", 3)
meta_p53_RUV <- str_split_fixed(colnames(logFC_mat_p53_RUV), "_", 2)
col_annot_p53_RUV <- HeatmapAnnotation(
  Drug = meta_p53_RUV[, 1],
  Time = meta_p53_RUV[, 2],
  col = list(
    Drug = c("DOX" = "#499FBD"),
    Time = c("24T" = "#238B45", 
             "24R" = "#74C476", 
             "144R" = "#C7E9C0")
  ),
  annotation_height = unit(c(1, 1, 1), "cm")
)

# Draw heatmap
Heatmap(logFC_mat_p53_RUV,
        name = "logFC",
        top_annotation = col_annot,
        cluster_columns = FALSE,
        cluster_rows = TRUE,
        show_row_names = TRUE,
        show_column_names = FALSE,
        layer_fun = function(j, i, x, y, width, height, fill) {
          grid.text(signif_mat_p53_RUV[cbind(i, j)], x, y, gp = gpar(fontsize = 9))
        },
        column_title = "P53 Target Genes Expression\nDOX Recovery (RUVs Corrected)",
        column_title_gp = gpar(fontsize = 14, fontface = "bold")
)

Past versions of "RUVs p53 Target Genes logFC HM-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##p53 logFC boxplots

#get an overall idea of the logFC of these genes over timepoints
# library(rstatix)
# Read p53 gene list - named p53_genes

# p53_genes <- readRDS("data/new/RUV/p53_genes_symbolentrez.RDS")
# 
# # Convert gene symbols to Entrez IDs
# p53_targets <- p53_genes %>%
#   mutate(Entrez_ID = mapIds(org.Hs.eg.db,
#                             keys = SYMBOL,
#                             column = "ENTREZID",
#                             keytype = "SYMBOL",
#                             multiVals = "first"))
# 
#p53_target_genes <- na.omit(p53_targets$Entrez_ID)

# saveRDS(p53_target_genes, "data/new/RUV/p53_target_genes_symbolentrez.RDS")
#this already has both SYMBOL and Entrez_ID

p53_target_genes <- readRDS("data/new/RUV/p53_target_genes_symbolentrez.RDS")

all_toptables_RUV <- bind_rows(
  DOX_24T_R %>% mutate(Drug = "DOX", Timepoint = "24T"),
  DOX_24R_R %>% mutate(Drug = "DOX", Timepoint = "24R"),
  DOX_144R_R %>% mutate(Drug = "DOX", Timepoint = "144R"),
)

filtered_toptables_RUV_p53 <- all_toptables_RUV %>%
  filter(Entrez_ID %in% p53_target_genes) %>%
  mutate(abs_logFC = abs(logFC)) 
  

filtered_toptables_RUV_p53 <- filtered_toptables_RUV_p53 %>%
  mutate(
    Drug = factor(Drug, levels = c("DOX")),
    Timepoint = factor(Timepoint, levels = c("24T", "24R", "144R"), 
                       labels = c("Timepoint: 24T", "Timepoint: 24R", "Timepoint: 144R"))
  )

wilcox_results_p53 <- filtered_toptables_RUV_p53 %>%
  wilcox_test(abs_logFC ~ Timepoint) %>%
  adjust_pvalue(method = "bonferroni") %>%
  mutate(significance = ifelse(p < 0.05, "*", "")) %>% 
  mutate(Conditions = paste(group1, "vs", group2, sep = " "))

#make a little thing of your timepoint comparisons
pairs_p53 <- wilcox_results_p53 %>% 
  dplyr::select(group1, group2) %>% 
  distinct()

max_per_timepoint_p53 <- filtered_toptables_RUV_p53 %>% 
  group_by(Timepoint) %>% 
  summarise(max_logFC = max(abs_logFC, na.rm = TRUE), .groups = "drop")
  
#Join max values for group1
star_positions_p53 <- pairs_p53 %>%
  left_join(max_per_timepoint_p53, by = c("group1" = "Timepoint"))
names(star_positions_p53)[names(star_positions_p53) == "max_logFC"] <- "max1"

#Join max values for group2, with suffixes to avoid name conflict
star_positions_p53 <- star_positions_p53 %>%
  left_join(max_per_timepoint_p53, by = c("group2" = "Timepoint"), suffix = c(".group1", ".group2"))
names(star_positions_p53)[names(star_positions_p53) == "max_logFC"] <- "max2"

star_positions_p53 <- star_positions_p53 %>% 
  mutate(y_pos = pmax(max1, max2, na.rm = TRUE) + 0.2)

#now star positions has the same group1 and group2 as wilcoxon

wilcox_results_plot_p53 <- wilcox_results_p53 %>%
  left_join(star_positions_p53, by = c("group1", "group2")) %>%
  mutate(x_position = 1.5)  

wilcox_results_plot_p53 <- wilcox_results_plot_p53 %>% 
  mutate(group1 = gsub("Timepoint: ", "", group1),
         group2 = gsub("Timepoint: ", "", group2))

wilcox_results_plot_p53 <- wilcox_results_plot_p53 %>%
  mutate(x_position = case_when(
    group1 == "24T" & group2 == "24R" ~ 1.5,
    group1 == "24T" & group2 == "144R" ~ 2,
    group1 == "24R" & group2 == "144R" ~ 2.5
  ))

####logFC####
ggplot(filtered_toptables_RUV_p53, aes(x = Timepoint, y = logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  # geom_text(
  #   data = wilcox_results_plot_p53, 
  #   aes(x = x_position, y = y_pos, label = significance), 
  #   size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  # ) +
  theme_bw() +
  xlab("") +
  ylab("Log Fold Change") +  
  ggtitle("Log Fold Change for p53 Target Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC Boxplots p53 RUVs-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

####abs logFC####
ggplot(filtered_toptables_RUV_p53, aes(x = Timepoint, y = abs_logFC, fill = Timepoint)) +
  geom_boxplot() +
  scale_fill_manual(values = c(
    "Timepoint: 24T" = "#238B45",
    "Timepoint: 24R" = "#74C476",
    "Timepoint: 144R" = "#C7E9C0")) +  
  facet_wrap(~ Drug) +  
  # geom_text(
  #   data = wilcox_results_plot_p53, 
  #   aes(x = x_position, y = y_pos, label = significance), 
  #   size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
  # ) +
  theme_bw() +
  xlab("") +
  ylab("|Log Fold Change|") +  
  ggtitle("|Log Fold Change| for p53 Target Genes") +
  theme(
    plot.title = element_text(size = rel(1.5), hjust = 0.5),
    axis.title = element_text(size = 15, color = "black"),
    axis.line = element_line(linewidth = 1.5),
    strip.background = element_rect(fill = "gray"),  
    strip.text = element_text(size = 12, color = "black", face = "bold"),  
    axis.text.x = element_text(size = 8, color = "black", angle = 0)
  )

Past versions of "logFC Boxplots p53 RUVs-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

###logFC boxplots with all timepoint comparisons wilcoxon

# #try this where each of my timepoints are compared like the wilcoxon test - plot all of these and see which are significant
# 
# Comparisons <- tribble(
#   ~group1, ~group2,
#   "24T",   "24R",
#   "24T",   "144R",
#   "24R",   "144R"
# )
# 
# # Expand your filtered_toptables_RUV_p53 to include comparisons
# filtered_toptables_RUV_p53_comp <- filtered_toptables_RUV_p53 %>%
#   # Create a cross join with the comparisons
#   crossing(Comparisons) %>%
#   # Keep only the rows where the gene's timepoint matches one of the groups in the comparison
#   filter(Timepoint %in% c(group1, group2)) %>%
#   mutate(
#     Conditions = factor(paste(group1, "vs", group2),
#                         levels = c("24T vs 24R", "24T vs 144R", "24R vs 144R"))
#   )
# 
# 
# # filtered_toptables_RUV_p53_comp <- filtered_toptables_RUV_p53_comp %>%
# #   mutate(
# #     Drug = factor(Drug, levels = c("DOX")),
# #     Timepoint_raw = Timepoint,  #save unmod version(24T, 24R, 144R)
# #     Timepoint = factor(Timepoint, levels = c("24T", "24R", "144R"), 
# #                        labels = c("24T", "24R", "144R")),
# #     Conditions = factor(paste(group1, "vs", group2),
# #                         levels = c("24T vs 24R", "24T vs 144R", "24R vs 144R"))
# #   )
# 
# wilcox_results_p53 <- filtered_toptables_RUV_p53_comp %>%
#   wilcox_test(abs_logFC ~ Timepoint) %>%
#   adjust_pvalue(method = "bonferroni") %>%
#   mutate(significance = ifelse(p < 0.05, "*", "")) %>% 
#   mutate(Comparisons = paste(group1, "vs", group2, sep = " "))
# 
# #make a little thing of your timepoint comparisons
# pairs_p53 <- wilcox_results_p53 %>% 
#   dplyr::select(group1, group2) %>% 
#   distinct()
# 
# max_per_timepoint_p53 <- filtered_toptables_RUV_p53_comp %>% 
#   group_by(Timepoint) %>% 
#   summarise(max_logFC = max(abs_logFC, na.rm = TRUE), .groups = "drop")
#   
# #Join max values for group1
# star_positions_p53 <- pairs_p53 %>%
#   left_join(max_per_timepoint_p53, by = c("group1" = "Timepoint"))
# names(star_positions_p53)[names(star_positions_p53) == "max_logFC"] <- "max1"
# 
# #Join max values for group2, with suffixes to avoid name conflict
# star_positions_p53 <- star_positions_p53 %>%
#   left_join(max_per_timepoint_p53, by = c("group2" = "Timepoint"), suffix = c(".group1", ".group2"))
# names(star_positions_p53)[names(star_positions_p53) == "max_logFC"] <- "max2"
# 
# star_positions_p53 <- star_positions_p53 %>% 
#   mutate(y_pos = pmax(max1, max2, na.rm = TRUE) + 0.2)
# 
# #now star positions has the same group1 and group2 as wilcoxon
# 
# wilcox_results_plot_p53 <- wilcox_results_p53 %>%
#   left_join(star_positions_p53, by = c("group1", "group2")) %>%
#   mutate(x_position = 1.5)  
# 
# wilcox_results_plot_p53 <- wilcox_results_plot_p53 %>% 
#   mutate(group1 = gsub("Timepoint: ", "", group1),
#          group2 = gsub("Timepoint: ", "", group2))
# 
# wilcox_results_plot_p53 <- wilcox_results_plot_p53 %>%
#   mutate(
#     group1_raw = str_remove(group1, "^Timepoint: "),
#     group2_raw = str_remove(group2, "^Timepoint: ")
#   )
# 
# wilcox_results_plot_p53 <- wilcox_results_plot_p53 %>%
#   mutate(x_position = case_when(
#     group1 == "24T" & group2 == "24R" ~ 1.5,
#     group1 == "24T" & group2 == "144R" ~ 2,
#     group1 == "24R" & group2 == "144R" ~ 2.5
#   ))
# 
# ####logFC####
# ggplot(filtered_toptables_RUV_p53_comp, aes(x = Timepoint, y = logFC, fill = Timepoint)) +
#   geom_boxplot() +
#   scale_fill_manual(values = c(
#     "24T" = "#238B45",
#     "24R" = "#74C476",
#     "144R" = "#C7E9C0")) +  
#   facet_wrap(~Conditions) +  
#   geom_text(
#     data = wilcox_results_plot_p53, 
#     aes(x = x_position, y = y_pos, label = significance), 
#     size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
#   ) +
#   theme_bw() +
#   xlab("") +
#   ylab("Log Fold Change") +  
#   ggtitle("Log Fold Change for p53 Target Genes") +
#   theme(
#     plot.title = element_text(size = rel(1.5), hjust = 0.5),
#     axis.title = element_text(size = 15, color = "black"),
#     axis.line = element_line(linewidth = 1.5),
#     strip.background = element_rect(fill = "gray"),  
#     strip.text = element_text(size = 12, color = "black", face = "bold"),  
#     axis.text.x = element_text(size = 8, color = "black", angle = 0)
#   )
# 
# ####abs logFC####
# ggplot(filtered_toptables_RUV_p53_comp, aes(x = Conditions, y = abs_logFC, fill = Timepoint)) +
#   geom_boxplot() +
#   scale_fill_manual(values = c(
#     "24T" = "#238B45",
#     "24R" = "#74C476",
#     "144R" = "#C7E9C0")) +  
#   facet_grid(~Conditions) +  
#   geom_text(
#     data = wilcox_results_plot_p53, 
#     aes(x = x_position, y = y_pos, label = significance), 
#     size = 6, fontface = "bold", color = "black", inherit.aes = FALSE
#   ) +
#   theme_bw() +
#   xlab("") +
#   ylab("|Log Fold Change|") +  
#   ggtitle("|Log Fold Change| for p53 Target Genes") +
#   theme(
#     plot.title = element_text(size = rel(1.5), hjust = 0.5),
#     axis.title = element_text(size = 15, color = "black"),
#     axis.line = element_line(linewidth = 1.5),
#     strip.background = element_rect(fill = "gray"),  
#     strip.text = element_text(size = 12, color = "black", face = "bold"),  
#     axis.text.x = element_text(size = 8, color = "black", angle = 0)
#   )

#Read in my DEGs Data

#read in boxplot1 for my log2cpm data
boxplot1 <- read.csv("data/new/filcpm_final_matrix.csv") %>% 
  as.data.frame()
#this dataframe is unchanged

# Load Toptables
deg_files_ruv <- list.files("data/new/DEGs", pattern = "Toptable_RUV.*\\.csv", full.names = TRUE)
deg_list_ruv <- lapply(deg_files_ruv, read.csv)
names(deg_list_ruv) <- gsub("data/DEGs/Toptable_|\\.csv", "", deg_files_ruv)  

# Function to check significance based on **Entrez_ID in the correct sample**
is_significant <- function(gene, drug, conc, timepoint) {
  condition <- paste(drug, conc, timepoint, sep = "_")
  if (!condition %in% names(deg_list_ruv)) return(FALSE)
  
  toptable <- deg_list[[condition]]
  gene_entrez <- boxplot1$ENTREZID[boxplot1$SYMBOL == gene]
  
  if (length(gene_entrez) == 0) return(FALSE)
  
  return(any(gene_entrez %in% toptable$Entrez_ID[toptable$adj.P.Val < 0.05]))
}

##Process Data for Plotting RUVs logFC Boxplots

process_gene_data_DDR_RUVs_boxplots <- function(gene) {
  gene_data_boxplots_RUVs <- boxplot1 %>% filter(SYMBOL == gene)
  # Reshape data
  long_data_RUV_DDR <- gene_data_boxplots_RUVs %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6R$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, Indv, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
    # Identify significant conditions **per Drug, Conc, and Timepoint**
  significance_labels <- long_data_RUV_DDR %>%
    distinct(Drug, Timepoint, Indv) %>%
    rowwise() %>%
    mutate(
      max_log2CPM = max(long_data_RUV_DDR$log2CPM[long_data_RUV_DDR$Condition == Condition], na.rm = TRUE),
      Significance = ifelse(is_significant(gene, Drug, Timepoint, Indv), "*", "")
    ) %>%
    filter(Significance != "") %>% ungroup()
  
  list(long_data_RUV_DDR = long_data_RUV_DDR, significance_labels = significance_labels)
}

#####now I can go ahead and generate boxplots as requested
#want one for DDR, one for DIC, and one for p53

#genelists:
DDR_genes_ruv <- all_data_DDR_RUV$Gene
DIC_genes_ruv <- all_data_DIC_RUV$Gene
p53_genes_ruv <- all_data_p53_RUV$Gene

# #Generate Boxplots from the above function using our gene lists above
# for (gene in boxplot1) {
#   gene_data_boxplots_RUVs <- process_top5_D24R_1(gene)
#   p <- ggplot(gene_data_boxplots_RUVs, aes(x = Condition, y = log2cpm, fill = Drug)) +
#     geom_boxplot(outlier.shape = NA) +
#     geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
#     scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
#     ggtitle(paste("Log2cpm", gene, "top5DEGs D24R RUVs")) +
#     labs(x = "Treatment", y = "log2cpm") +
#     theme_bw() +
#     theme(
#       plot.title = element_text(size = rel(2), hjust = 0.5),
#       axis.title = element_text(size = 15, color = "black"),
#       axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
#     )
#   print(p)
# }

#Cormotif Function

## Fit limma model using code as it is found in the original cormotif code. It has
## only been modified to add names to the matrix of t values, as well as the
## limma fits

limmafit.default <- function(exprs,groupid,compid) {
  limmafits  <- list()
  compnum    <- nrow(compid)
  genenum    <- nrow(exprs)
  limmat     <- matrix(0,genenum,compnum)
  limmas2    <- rep(0,compnum)
  limmadf    <- rep(0,compnum)
  limmav0    <- rep(0,compnum)
  limmag1num <- rep(0,compnum)
  limmag2num <- rep(0,compnum)

  rownames(limmat)  <- rownames(exprs)
  colnames(limmat)  <- rownames(compid)
  names(limmas2)    <- rownames(compid)
  names(limmadf)    <- rownames(compid)
  names(limmav0)    <- rownames(compid)
  names(limmag1num) <- rownames(compid)
  names(limmag2num) <- rownames(compid)

  for(i in 1:compnum) {
    selid1 <- which(groupid == compid[i,1])
    selid2 <- which(groupid == compid[i,2])
    eset   <- new("ExpressionSet", exprs=cbind(exprs[,selid1],exprs[,selid2]))
    g1num  <- length(selid1)
    g2num  <- length(selid2)
    designmat <- cbind(base=rep(1,(g1num+g2num)), delta=c(rep(0,g1num),rep(1,g2num)))
    fit <- lmFit(eset,designmat)
    fit <- eBayes(fit)
    limmat[,i] <- fit$t[,2]
    limmas2[i] <- fit$s2.prior
    limmadf[i] <- fit$df.prior
    limmav0[i] <- fit$var.prior[2]
    limmag1num[i] <- g1num
    limmag2num[i] <- g2num
    limmafits[[i]] <- fit

    # log odds
    # w<-sqrt(1+fit$var.prior[2]/(1/g1num+1/g2num))
    # log(0.99)+dt(fit$t[1,2],g1num+g2num-2+fit$df.prior,log=TRUE)-log(0.01)-dt(fit$t[1,2]/w, g1num+g2num-2+fit$df.prior, log=TRUE)+log(w)
  }
  names(limmafits) <- rownames(compid)
  limmacompnum<-nrow(compid)
  result<-list(t       = limmat,
               v0      = limmav0,
               df0     = limmadf,
               s20     = limmas2,
               g1num   = limmag1num,
               g2num   = limmag2num,
               compnum = limmacompnum,
               fits    = limmafits)
}

limmafit.counts <-
  function (exprs, groupid, compid, norm.factor.method = "TMM", voom.normalize.method = "none")
  {
    limmafits  <- list()
    compnum    <- nrow(compid)
    genenum    <- nrow(exprs)
    limmat     <- matrix(NA,genenum,compnum)
    limmas2    <- rep(0,compnum)
    limmadf    <- rep(0,compnum)
    limmav0    <- rep(0,compnum)
    limmag1num <- rep(0,compnum)
    limmag2num <- rep(0,compnum)

    rownames(limmat)  <- rownames(exprs)
    colnames(limmat)  <- rownames(compid)
    names(limmas2)    <- rownames(compid)
    names(limmadf)    <- rownames(compid)
    names(limmav0)    <- rownames(compid)
    names(limmag1num) <- rownames(compid)
    names(limmag2num) <- rownames(compid)

    for (i in 1:compnum) {
      message(paste("Running limma for comparision",i,"/",compnum))
      selid1 <- which(groupid == compid[i, 1])
      selid2 <- which(groupid == compid[i, 2])
      # make a new count data frame
      counts <- cbind(exprs[, selid1], exprs[, selid2])

      # remove NAs
      not.nas <- which(apply(counts, 1, function(x) !any(is.na(x))) == TRUE)

      # runn voom/limma
      d <- DGEList(counts[not.nas,])
      d <- calcNormFactors(d, method = norm.factor.method)
      g1num <- length(selid1)
      g2num <- length(selid2)
      designmat <- cbind(base = rep(1, (g1num + g2num)), delta = c(rep(0,
                                                                       g1num), rep(1, g2num)))

      y <- voom(d, designmat, normalize.method = voom.normalize.method)
      fit <- lmFit(y, designmat)
      fit <- eBayes(fit)

      limmafits[[i]] <- fit
      limmat[not.nas, i] <- fit$t[, 2]
      limmas2[i] <- fit$s2.prior
      limmadf[i] <- fit$df.prior
      limmav0[i] <- fit$var.prior[2]
      limmag1num[i] <- g1num
      limmag2num[i] <- g2num
    }
    limmacompnum <- nrow(compid)
    names(limmafits) <- rownames(compid)
    result <- list(t       = limmat,
                   v0      = limmav0,
                   df0     = limmadf,
                   s20     = limmas2,
                   g1num   = limmag1num,
                   g2num   = limmag2num,
                   compnum = limmacompnum,
                   fits    = limmafits)
  }

limmafit.list <-
  function (fitlist, cmp.idx=2)
  {
    compnum    <- length(fitlist)

    genes <- c()
    for (i in 1:compnum) genes <- unique(c(genes, rownames(fitlist[[i]])))

    genenum    <- length(genes)
    limmat     <- matrix(NA,genenum,compnum)
    limmas2    <- rep(0,compnum)
    limmadf    <- rep(0,compnum)
    limmav0    <- rep(0,compnum)
    limmag1num <- rep(0,compnum)
    limmag2num <- rep(0,compnum)

    rownames(limmat)  <- genes
    colnames(limmat)  <- names(fitlist)
    names(limmas2)    <- names(fitlist)
    names(limmadf)    <- names(fitlist)
    names(limmav0)    <- names(fitlist)
    names(limmag1num) <- names(fitlist)
    names(limmag2num) <- names(fitlist)

    for (i in 1:compnum) {
      this.t <- fitlist[[i]]$t[,cmp.idx]
      limmat[names(this.t),i] <- this.t

      limmas2[i]    <- fitlist[[i]]$s2.prior
      limmadf[i]    <- fitlist[[i]]$df.prior
      limmav0[i]    <- fitlist[[i]]$var.prior[cmp.idx]
      limmag1num[i] <- sum(fitlist[[i]]$design[,cmp.idx]==0)
      limmag2num[i] <- sum(fitlist[[i]]$design[,cmp.idx]==1)
    }

    limmacompnum <- compnum
    result <- list(t       = limmat,
                   v0      = limmav0,
                   df0     = limmadf,
                   s20     = limmas2,
                   g1num   = limmag1num,
                   g2num   = limmag2num,
                   compnum = limmacompnum,
                   fits    = limmafits)

  }

## Rank genes based on statistics
generank<-function(x) {
  xcol<-ncol(x)
  xrow<-nrow(x)
  result<-matrix(0,xrow,xcol)
  z<-(1:1:xrow)
  for(i in 1:xcol) {
    y<-sort(x[,i],decreasing=TRUE,na.last=TRUE)
    result[,i]<-match(x[,i],y)
    result[,i]<-order(result[,i])
  }
  result
}

## Log-likelihood for moderated t under H0
modt.f0.loglike<-function(x,df) {
  a<-dt(x, df, log=TRUE)
  result<-as.vector(a)
  flag<-which(is.na(result)==TRUE)
  result[flag]<-0
  result
}

## Log-likelihood for moderated t under H1
## param=c(df,g1num,g2num,v0)
modt.f1.loglike<-function(x,param) {
  df<-param[1]
  g1num<-param[2]
  g2num<-param[3]
  v0<-param[4]
  w<-sqrt(1+v0/(1/g1num+1/g2num))
  dt(x/w, df, log=TRUE)-log(w)
  a<-dt(x/w, df, log=TRUE)-log(w)
  result<-as.vector(a)
  flag<-which(is.na(result)==TRUE)
  result[flag]<-0
  result
}

## Correlation Motif Fit
cmfit.X<-function(x, type, K=1, tol=1e-3, max.iter=100) {
  ## initialize
  xrow <- nrow(x)
  xcol <- ncol(x)
  loglike0 <- list()
  loglike1 <- list()
  p <- rep(1, K)/K
  q <- matrix(runif(K * xcol), K, xcol)
  q[1, ] <- rep(0.01, xcol)
  for (i in 1:xcol) {
    f0 <- type[[i]][[1]]
    f0param <- type[[i]][[2]]
    f1 <- type[[i]][[3]]
    f1param <- type[[i]][[4]]
    loglike0[[i]] <- f0(x[, i], f0param)
    loglike1[[i]] <- f1(x[, i], f1param)
  }
  condlike <- list()
  for (i in 1:xcol) {
    condlike[[i]] <- matrix(0, xrow, K)
  }
  loglike.old <- -1e+10
  for (i.iter in 1:max.iter) {
    if ((i.iter%%50) == 0) {
      print(paste("We have run the first ", i.iter, " iterations for K=",
                  K, sep = ""))
    }
    err <- tol + 1
    clustlike <- matrix(0, xrow, K)
    #templike <- matrix(0, xrow, 2)
    templike1 <- rep(0, xrow)
    templike2 <- rep(0, xrow)
    for (j in 1:K) {
      for (i in 1:xcol) {
        templike1 <- log(q[j, i]) + loglike1[[i]]
        templike2 <- log(1 - q[j, i]) + loglike0[[i]]
        tempmax <- Rfast::Pmax(templike1, templike2)

        templike1 <- exp(templike1 - tempmax)
        templike2 <- exp(templike2 - tempmax)

        tempsum <- templike1 + templike2
        clustlike[, j] <- clustlike[, j] + tempmax +
          log(tempsum)
        condlike[[i]][, j] <- templike1/tempsum
      }
      clustlike[, j] <- clustlike[, j] + log(p[j])
    }
    #tempmax <- apply(clustlike, 1, max)
    tempmax <- Rfast::rowMaxs(clustlike, value=TRUE)
    for (j in 1:K) {
      clustlike[, j] <- exp(clustlike[, j] - tempmax)
    }
    #tempsum <- apply(clustlike, 1, sum)
    tempsum <- Rfast::rowsums(clustlike)
    for (j in 1:K) {
      clustlike[, j] <- clustlike[, j]/tempsum
    }
    #p.new <- (apply(clustlike, 2, sum) + 1)/(xrow + K)
    p.new <- (Rfast::colsums(clustlike) + 1)/(xrow + K)
    q.new <- matrix(0, K, xcol)
    for (j in 1:K) {
      clustpsum <- sum(clustlike[, j])
      for (i in 1:xcol) {
        q.new[j, i] <- (sum(clustlike[, j] * condlike[[i]][,
                                                           j]) + 1)/(clustpsum + 2)
      }
    }
    err.p <- max(abs(p.new - p)/p)
    err.q <- max(abs(q.new - q)/q)
    err <- max(err.p, err.q)
    loglike.new <- (sum(tempmax + log(tempsum)) + sum(log(p.new)) +
                      sum(log(q.new) + log(1 - q.new)))/xrow
    p <- p.new
    q <- q.new
    loglike.old <- loglike.new
    if (err < tol) {
      break
    }
  }
  clustlike <- matrix(0, xrow, K)
  for (j in 1:K) {
    for (i in 1:xcol) {
      templike1 <- log(q[j, i]) + loglike1[[i]]
      templike2 <- log(1 - q[j, i]) + loglike0[[i]]
      tempmax <- Rfast::Pmax(templike1, templike2)

      templike1 <- exp(templike1 - tempmax)
      templike2 <- exp(templike2 - tempmax)

      tempsum <- templike1 + templike2
      clustlike[, j] <- clustlike[, j] + tempmax + log(tempsum)
      condlike[[i]][, j] <- templike1/tempsum
    }
    clustlike[, j] <- clustlike[, j] + log(p[j])
  }
  #tempmax <- apply(clustlike, 1, max)
  tempmax <- Rfast::rowMaxs(clustlike, value=TRUE)
  for (j in 1:K) {
    clustlike[, j] <- exp(clustlike[, j] - tempmax)
  }
  #tempsum <- apply(clustlike, 1, sum)
  tempsum <- Rfast::rowsums(clustlike)
  for (j in 1:K) {
    clustlike[, j] <- clustlike[, j]/tempsum
  }
  p.post <- matrix(0, xrow, xcol)
  for (j in 1:K) {
    for (i in 1:xcol) {
      p.post[, i] <- p.post[, i] + clustlike[, j] * condlike[[i]][,
                                                                  j]
    }
  }
  loglike.old <- loglike.old - (sum(log(p)) + sum(log(q) +
                                                    log(1 - q)))/xrow
  loglike.old <- loglike.old * xrow
  result <- list(p.post = p.post, motif.prior = p, motif.q = q,
                 loglike = loglike.old, clustlike=clustlike, condlike=condlike)
}

## Fit using (0,0,...,0) and (1,1,...,1)
cmfitall<-function(x, type, tol=1e-3, max.iter=100) {
  ## initialize
  xrow<-nrow(x)
  xcol<-ncol(x)
  loglike0<-list()
  loglike1<-list()
  p<-0.01

  ## compute loglikelihood
  L0<-matrix(0,xrow,1)
  L1<-matrix(0,xrow,1)
  for(i in 1:xcol) {
    f0<-type[[i]][[1]]
    f0param<-type[[i]][[2]]
    f1<-type[[i]][[3]]
    f1param<-type[[i]][[4]]
    loglike0[[i]]<-f0(x[,i],f0param)
    loglike1[[i]]<-f1(x[,i],f1param)
    L0<-L0+loglike0[[i]]
    L1<-L1+loglike1[[i]]
  }


  ## EM algorithm to get MLE of p and q
  loglike.old <- -1e10
  for(i.iter in 1:max.iter) {
    if((i.iter%%50) == 0) {
      print(paste("We have run the first ", i.iter, " iterations",sep=""))
    }
    err<-tol+1

    ## compute posterior cluster membership
    clustlike<-matrix(0,xrow,2)
    clustlike[,1]<-log(1-p)+L0
    clustlike[,2]<-log(p)+L1

    tempmax<-apply(clustlike,1,max)
    for(j in 1:2) {
      clustlike[,j]<-exp(clustlike[,j]-tempmax)
    }
    tempsum<-apply(clustlike,1,sum)

    ## update motif occurrence rate
    for(j in 1:2) {
      clustlike[,j]<-clustlike[,j]/tempsum
    }

    p.new<-(sum(clustlike[,2])+1)/(xrow+2)

    ## evaluate convergence
    err<-abs(p.new-p)/p

    ## evaluate whether the log.likelihood increases
    loglike.new<-(sum(tempmax+log(tempsum))+log(p.new)+log(1-p.new))/xrow

    loglike.old<-loglike.new
    p<-p.new

    if(err<tol) {
      break;
    }
  }

  ## compute posterior p
  clustlike<-matrix(0,xrow,2)
  clustlike[,1]<-log(1-p)+L0
  clustlike[,2]<-log(p)+L1

  tempmax<-apply(clustlike,1,max)
  for(j in 1:2) {
    clustlike[,j]<-exp(clustlike[,j]-tempmax)
  }
  tempsum<-apply(clustlike,1,sum)

  for(j in 1:2) {
    clustlike[,j]<-clustlike[,j]/tempsum
  }

  p.post<-matrix(0,xrow,xcol)
  for(i in 1:xcol) {
    p.post[,i]<-clustlike[,2]
  }

  ## return

  #calculate back loglikelihood
  loglike.old<-loglike.old-(log(p)+log(1-p))/xrow
  loglike.old<-loglike.old*xrow
  result<-list(p.post=p.post, motif.prior=p, loglike=loglike.old)
}

## Fit each dataset separately
cmfitsep<-function(x, type, tol=1e-3, max.iter=100) {
  ## initialize
  xrow<-nrow(x)
  xcol<-ncol(x)
  loglike0<-list()
  loglike1<-list()
  p<-0.01*rep(1,xcol)
  loglike.final<-rep(0,xcol)

  ## compute loglikelihood
  for(i in 1:xcol) {
    f0<-type[[i]][[1]]
    f0param<-type[[i]][[2]]
    f1<-type[[i]][[3]]
    f1param<-type[[i]][[4]]
    loglike0[[i]]<-f0(x[,i],f0param)
    loglike1[[i]]<-f1(x[,i],f1param)
  }

  p.post<-matrix(0,xrow,xcol)

  ## EM algorithm to get MLE of p
  for(coli in 1:xcol) {
    loglike.old <- -1e10
    for(i.iter in 1:max.iter) {
      if((i.iter%%50) == 0) {
        print(paste("We have run the first ", i.iter, " iterations",sep=""))
      }
      err<-tol+1

      ## compute posterior cluster membership
      clustlike<-matrix(0,xrow,2)
      clustlike[,1]<-log(1-p[coli])+loglike0[[coli]]
      clustlike[,2]<-log(p[coli])+loglike1[[coli]]

      tempmax<-apply(clustlike,1,max)
      for(j in 1:2) {
        clustlike[,j]<-exp(clustlike[,j]-tempmax)
      }
      tempsum<-apply(clustlike,1,sum)

      ## evaluate whether the log.likelihood increases
      loglike.new<-sum(tempmax+log(tempsum))/xrow

      ## update motif occurrence rate
      for(j in 1:2) {
        clustlike[,j]<-clustlike[,j]/tempsum
      }

      p.new<-(sum(clustlike[,2]))/(xrow)

      ## evaluate convergence
      err<-abs(p.new-p[coli])/p[coli]
      loglike.old<-loglike.new
      p[coli]<-p.new

      if(err<tol) {
        break;
      }
    }

    ## compute posterior p
    clustlike<-matrix(0,xrow,2)
    clustlike[,1]<-log(1-p[coli])+loglike0[[coli]]
    clustlike[,2]<-log(p[coli])+loglike1[[coli]]

    tempmax<-apply(clustlike,1,max)
    for(j in 1:2) {
      clustlike[,j]<-exp(clustlike[,j]-tempmax)
    }
    tempsum<-apply(clustlike,1,sum)

    for(j in 1:2) {
      clustlike[,j]<-clustlike[,j]/tempsum
    }

    p.post[,coli]<-clustlike[,2]
    loglike.final[coli]<-loglike.old
  }


  ## return
  loglike.final<-loglike.final*xrow
  result<-list(p.post=p.post, motif.prior=p, loglike=loglike.final)
}

## Fit the full model
cmfitfull<-function(x, type, tol=1e-3, max.iter=100) {
  ## initialize
  xrow<-nrow(x)
  xcol<-ncol(x)
  loglike0<-list()
  loglike1<-list()
  K<-2^xcol
  p<-rep(1,K)/K
  pattern<-rep(0,xcol)
  patid<-matrix(0,K,xcol)

  ## compute loglikelihood
  for(i in 1:xcol) {
    f0<-type[[i]][[1]]
    f0param<-type[[i]][[2]]
    f1<-type[[i]][[3]]
    f1param<-type[[i]][[4]]
    loglike0[[i]]<-f0(x[,i],f0param)
    loglike1[[i]]<-f1(x[,i],f1param)
  }
  L<-matrix(0,xrow,K)
  for(i in 1:K)
  {
    patid[i,]<-pattern
    for(j in 1:xcol) {
      if(pattern[j] < 0.5) {
        L[,i]<-L[,i]+loglike0[[j]]
      } else {
        L[,i]<-L[,i]+loglike1[[j]]
      }
    }

    if(i < K) {
      pattern[xcol]<-pattern[xcol]+1
      j<-xcol
      while(pattern[j] > 1) {
        pattern[j]<-0
        j<-j-1
        pattern[j]<-pattern[j]+1
      }
    }
  }

  ## EM algorithm to get MLE of p and q
  loglike.old <- -1e10
  for(i.iter in 1:max.iter) {
    if((i.iter%%50) == 0) {
      print(paste("We have run the first ", i.iter, " iterations",sep=""))
    }
    err<-tol+1

    ## compute posterior cluster membership
    clustlike<-matrix(0,xrow,K)
    for(j in 1:K) {
      clustlike[,j]<-log(p[j])+L[,j]
    }

    tempmax<-apply(clustlike,1,max)
    for(j in 1:K) {
      clustlike[,j]<-exp(clustlike[,j]-tempmax)
    }
    tempsum<-apply(clustlike,1,sum)

    ## update motif occurrence rate
    for(j in 1:K) {
      clustlike[,j]<-clustlike[,j]/tempsum
    }

    p.new<-(apply(clustlike,2,sum)+1)/(xrow+K)

    ## evaluate convergence
    err<-max(abs(p.new-p)/p)

    ## evaluate whether the log.likelihood increases
    loglike.new<-(sum(tempmax+log(tempsum))+sum(log(p.new)))/xrow

    loglike.old<-loglike.new
    p<-p.new

    if(err<tol) {
      break;
    }
  }

  ## compute posterior p
  clustlike<-matrix(0,xrow,K)
  for(j in 1:K) {
    clustlike[,j]<-log(p[j])+L[,j]
  }

  tempmax<-apply(clustlike,1,max)
  for(j in 1:K) {
    clustlike[,j]<-exp(clustlike[,j]-tempmax)
  }
  tempsum<-apply(clustlike,1,sum)

  for(j in 1:K) {
    clustlike[,j]<-clustlike[,j]/tempsum
  }

  p.post<-matrix(0,xrow,xcol)
  for(j in 1:K) {
    for(i in 1:xcol) {
      if(patid[j,i] > 0.5) {
        p.post[,i]<-p.post[,i]+clustlike[,j]
      }
    }
  }

  ## return
  #calculate back loglikelihood
  loglike.old<-loglike.old-sum(log(p))/xrow
  loglike.old<-loglike.old*xrow
  result<-list(p.post=p.post, motif.prior=p, loglike=loglike.old)
}

generatetype<-function(limfitted)
{
  jtype<-list()
  df<-limfitted$g1num+limfitted$g2num-2+limfitted$df0
  for(j in 1:limfitted$compnum)
  {
    jtype[[j]]<-list(f0=modt.f0.loglike, f0.param=df[j], f1=modt.f1.loglike, f1.param=c(df[j],limfitted$g1num[j],limfitted$g2num[j],limfitted$v0[j]))
  }
  jtype
}

cormotiffit <- function(exprs, groupid=NULL, compid=NULL, K=1, tol=1e-3,
                        max.iter=100, BIC=TRUE, norm.factor.method="TMM",
                        voom.normalize.method = "none", runtype=c("logCPM","counts","limmafits"), each=3)
{
  # first I want to do some typechecking. Input can be either a normalized
  # matrix, a count matrix, or a list of limma fits. Dispatch the correct
  # limmafit accordingly.
  # todo: add some typechecking here
  limfitted <- list()
  if (runtype=="counts") {DOX_24T_shared_DEGs
    limfitted <- limmafit.counts(exprs,groupid,compid, norm.factor.method, voom.normalize.method)
  } else if (runtype=="logCPM") {
    limfitted <- limmafit.default(exprs,groupid,compid)
  } else if (runtype=="limmafits") {
    limfitted <- limmafit.list(exprs)
  } else {
    stop("runtype must be one of 'logCPM', 'counts', or 'limmafits'")
  }


  jtype<-generatetype(limfitted)
  fitresult<-list()
  ks <- rep(K, each = each)
  fitresult <- bplapply(1:length(ks), function(i, x, type, ks, tol, max.iter) {
    cmfit.X(x, type, K = ks[i], tol = tol, max.iter = max.iter)
  }, x=limfitted$t, type=jtype, ks=ks, tol=tol, max.iter=max.iter)

  best.fitresults <- list()
  for (i in 1:length(K)) {
    w.k <- which(ks==K[i])
    this.bic <- c()
    for (j in w.k) this.bic[j] <- -2 * fitresult[[j]]$loglike + (K[i] - 1 + K[i] * limfitted$compnum) * log(dim(limfitted$t)[1])
    w.min <- which(this.bic == min(this.bic, na.rm = TRUE))[1]
    best.fitresults[[i]] <- fitresult[[w.min]]
  }
  fitresult <- best.fitresults

  bic <- rep(0, length(K))
  aic <- rep(0, length(K))
  loglike <- rep(0, length(K))
  for (i in 1:length(K)) loglike[i] <- fitresult[[i]]$loglike
  for (i in 1:length(K)) bic[i] <- -2 * fitresult[[i]]$loglike + (K[i] - 1 + K[i] * limfitted$compnum) * log(dim(limfitted$t)[1])
  for (i in 1:length(K)) aic[i] <- -2 * fitresult[[i]]$loglike + 2 * (K[i] - 1 + K[i] * limfitted$compnum)
  if(BIC==TRUE) {
    bestflag=which(bic==min(bic))
  }
  else {
    bestflag=which(aic==min(aic))
  }
  result<-list(bestmotif=fitresult[[bestflag]],bic=cbind(K,bic),
               aic=cbind(K,aic),loglike=cbind(K,loglike), allmotifs=fitresult)

}

cormotiffitall<-function(exprs,groupid,compid, tol=1e-3, max.iter=100)
{
  limfitted<-limmafit(exprs,groupid,compid)
  jtype<-generatetype(limfitted)
  fitresult<-cmfitall(limfitted$t,type=jtype,tol=1e-3,max.iter=max.iter)
}

cormotiffitsep<-function(exprs,groupid,compid, tol=1e-3, max.iter=100)
{
  limfitted<-limmafit(exprs,groupid,compid)
  jtype<-generatetype(limfitted)
  fitresult<-cmfitsep(limfitted$t,type=jtype,tol=1e-3,max.iter=max.iter)
}

cormotiffitfull<-function(exprs,groupid,compid, tol=1e-3, max.iter=100)
{
  limfitted<-limmafit(exprs,groupid,compid)
  jtype<-generatetype(limfitted)
  fitresult<-cmfitfull(limfitted$t,type=jtype,tol=1e-3,max.iter=max.iter)
}

plotIC<-function(fitted_cormotif)
{
  oldpar<-par(mfrow=c(1,2))
  plot(fitted_cormotif$bic[,1], fitted_cormotif$bic[,2], type="b",xlab="Motif Number", ylab="BIC", main="BIC")
  plot(fitted_cormotif$aic[,1], fitted_cormotif$aic[,2], type="b",xlab="Motif Number", ylab="AIC", main="AIC")
}

plotMotif<-function(fitted_cormotif,title="")
{
  layout(matrix(1:2,ncol=2))
  u<-1:dim(fitted_cormotif$bestmotif$motif.q)[2]
  v<-1:dim(fitted_cormotif$bestmotif$motif.q)[1]
  image(u,v,t(fitted_cormotif$bestmotif$motif.q),
        col=gray(seq(from=1,to=0,by=-0.1)),xlab="Study",yaxt = "n",
        ylab="Corr. Motifs",main=paste(title,"pattern",sep=" "))
  axis(2,at=1:length(v))
  for(i in 1:(length(u)+1))
  {
    abline(v=(i-0.5))
  }
  for(i in 1:(length(v)+1))
  {
    abline(h=(i-0.5))
  }
  Ng=10000
  if(is.null(fitted_cormotif$bestmotif$p.post)!=TRUE)
    Ng=nrow(fitted_cormotif$bestmotif$p.post)
  genecount=floor(fitted_cormotif$bestmotif$motif.p*Ng)
  NK=nrow(fitted_cormotif$bestmotif$motif.q)
  plot(0,0.7,pch=".",xlim=c(0,1.2),ylim=c(0.75,NK+0.25),
       frame.plot=FALSE,axes=FALSE,xlab="No. of genes",ylab="", main=paste(title,"frequency",sep=" "))
  segments(0,0.7,fitted_cormotif$bestmotif$motif.p[1],0.7)
  rect(0,1:NK-0.3,fitted_cormotif$bestmotif$motif.p,1:NK+0.3,
       col="dark grey")
  mtext(1:NK,at=1:NK,side=2,cex=0.8)
  text(fitted_cormotif$bestmotif$motif.p+0.15,1:NK,
       labels=floor(fitted_cormotif$bestmotif$motif.p*Ng))
}

#Don't load me in if you're using the above function, as it has been modified above
#library(Cormotif)

##Input Data for Cormotif Original Matrix

#input the cormotif matrix you're going to use
##this should be tmm normalized log2cpm

#the matrix that I used previously for limma was TMM counts - cpm this
#dge was the name of the DGE list object

cormotif_test <- cpm(dge, log = TRUE)
colnames(cormotif_test) <- (Metadata_2$Final_sample_name)

cormotif_counts <- dge

cormotif_test_df <- cormotif_test %>% 
  as.data.frame() %>% 
  rownames_to_column(., var = "Entrez_ID")

#write.csv(cormotif_test, "data/new/Cormotif_test_matrix.csv")

#reorder my test matrix to match the new groupid I've made
#I want my columns to be in this order:
#DOX24T 1-6, DOX24R 1-6, DOX144R 1-6, DMSO24T 1-6, DMSO24R 1-6, DMSO144R 1-6
Cormotif <- read.csv("data/new/Cormotif_matrix_final.csv")
dim(Cormotif)

[1] 14319    37

#14319 genes across 37 cols (1 is Entrez_ID)
Cormotif_df <- data.frame(Cormotif)

rownames(Cormotif_df) <- Cormotif_df$Entrez_ID
exprs.cormotif <- as.matrix(Cormotif_df[,2:37])
dim(exprs.cormotif)

[1] 14319    36

#put together my group id and comparison id to make the correct comparisons between experimental conditions

#groupid tells which experimental conditions are grouped together
#compid tells which experimental conditions should be compared against one another
##ie DOX24T vs DMSO24T matched control

groupid_csv <- read.csv("data/new/GroupID.csv")
#now I have to make this into a vector (named vector)
groupid <- c(
  DOX_24T_1 = 1, 
  DOX_24T_2 = 1, 
  DOX_24T_3 = 1, 
  DOX_24T_4 = 1, 
  DOX_24T_5 = 1, 
  DOX_24T_6 = 1,
  DOX_24R_1 = 2, 
  DOX_24R_2 = 2, 
  DOX_24R_3 = 2, 
  DOX_24R_4 = 2, 
  DOX_24R_5 = 2, 
  DOX_24R_6 = 2,
  DOX_144R_1 = 3, 
  DOX_144R_2 = 3, 
  DOX_144R_3 = 3, 
  DOX_144R_4 = 3, 
  DOX_144R_5 = 3, 
  DOX_144R_6 = 3,
  DMSO_24T_1 = 4, 
  DMSO_24T_2 = 4, 
  DMSO_24T_3 = 4, 
  DMSO_24T_4 = 4, 
  DMSO_24T_5 = 4, 
  DMSO_24T_6 = 4,
  DMSO_24R_1 = 5, 
  DMSO_24R_2 = 5, 
  DMSO_24R_3 = 5, 
  DMSO_24R_4 = 5, 
  DMSO_24R_5 = 5, 
  DMSO_24R_6 = 5,
  DMSO_144R_1 = 6, 
  DMSO_144R_2 = 6, 
  DMSO_144R_3 = 6, 
  DMSO_144R_4 = 6, 
  DMSO_144R_5 = 6, 
  DMSO_144R_6 = 6
)
#saveRDS(groupid, "data/new/groupidCormotif.RDS")

compid <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))
#saveRDS(compid, "data/new/compidCormotif.RDS")

###Run Cormotif Original Data

#fit Cormotif model
# set.seed(19191)
#only set the seed ONCE

# motif.fitted_new <- cormotiffit(
#   exprs = exprs.cormotif,
#   groupid = groupid,
#   compid = compid,
#   K = 1:8,
#   max.iter = 1000,
#   BIC = TRUE,
#   runtype = "logCPM"
# )

# saveRDS(motif.fitted, "data/new/motif.fitted_new_250604.RDS")
motif.fitted <- readRDS("data/new/motif.fitted_final_3motif.RDS")

###Plotting Cormotif Original Data

#plot BIC and AIC to see which number of motifs was best for both models
plotIC(motif.fitted)

Past versions of "Plot Cormotif-1.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

motif.fitted$bic

     K      bic
[1,] 1 180063.9
[2,] 2 180034.4
[3,] 3 179813.4
[4,] 4 179855.6
[5,] 5 179895.7
[6,] 6 179936.2
[7,] 7 179976.6
[8,] 8 180020.3

#now plot the motifs themselves
plotMotif(motif.fitted, title = "Fitted Motifs for DXR")

Past versions of "Plot Cormotif-2.png"

Version	Author	Date
29a5c35	emmapfort	2025-05-16

#plot the probability legend
myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "Plot Cormotif-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###Extract the Gene Probabilities

#extract the posterior probability that these DEGs belong to motifs
gene_prob_all <- motif.fitted$bestmotif$p.post
rownames(gene_prob_all) <- rownames(Cormotif_df)

#assign each gene to a motif with max post prob
assigned_motifs <- apply(gene_prob_all, 1, which.max)
max_probs <- apply(gene_prob_all, 1, max)

#combine these into a dataframe - motif assigned genes (p.post)
motif_assignment_df <- gene_prob_all %>%
  as.data.frame() %>%
  rownames_to_column("Gene") %>%
  mutate(
    Assigned_Motif = assigned_motifs[Gene],
    Max_Probability = max_probs[Gene]
  )

#make some histograms of the unfiltered data from Cormotif p.post

gene_prob_all %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V1))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes p.post Distribution M1")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

gene_prob_all %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V2))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes p.post Distribution M2")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

gene_prob_all %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V3))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes p.post Distribution M3")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now change the probability cutoffs to get the ideal gene set with no overlaps

# Define gene probability groups
prob_all_1  <- rownames(gene_prob_all[(gene_prob_all[,1] >0.05 & gene_prob_all[,1] <0.3 & gene_prob_all[,2] <0.5 & gene_prob_all[,3] <0.5),])

length(prob_all_1)

[1] 5675

#5675

prob_all_2  <- rownames(gene_prob_all[(gene_prob_all[,1] >0.5 & gene_prob_all[,2] <0.5 & gene_prob_all[,3] <0.5),])

length(prob_all_2)

[1] 6353

#6353

prob_all_3  <- rownames(gene_prob_all[(gene_prob_all[,1] >0.3 & gene_prob_all[,1] <0.9 & gene_prob_all[,2] >0.5 & gene_prob_all[,3] >0.5),])

length(prob_all_3)

[1] 231

#231 genes with >0.3 <0.9 1

#compare between motif 1 and 2
mf1_genes <- prob_all_1
mf2_genes <- prob_all_2
mf3_genes <- prob_all_3

vennCor <- list(mf1_genes, mf2_genes, mf3_genes)
ggVennDiagram(
  vennCor,
  category.names = c("Motif 1", "Motif 2", "Motif 3")
) + ggtitle("Cormotif Specific and Shared DEGs p.post")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Extract gene probabilities-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#extract the cluster likelihood - which DEGs are most likely to be in this cluster
motif_prob <- motif.fitted$bestmotif$clustlike
rownames(motif_prob) <- rownames(gene_prob_all)
#write.csv(motif_prob,"data/new/cormotif_probability_genelist_all.csv")

#make some histograms to look at the distribution of clustlike genes without filtering
motif_prob %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V1))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes clustlike Distribution M1")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

motif_prob %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V2))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes clustlike Distribution M2")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

motif_prob %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V3))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes clustlike Distribution M3")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Extract gene probabilities-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

####try this Renee's way####
clust1_p <- motif_prob %>%
  as.data.frame() %>%
  filter(V1>0.5 & V2<0.5 & V3<0.5) %>% 
  rownames
clust2_p <- motif_prob %>%
  as.data.frame() %>%
  filter(V2>0.5 & V1<0.5 & V3<0.5) %>% 
  rownames
clust3_p <- motif_prob %>%
  as.data.frame() %>%
  filter(V3>0.5 & V1 <0.5 & V2 <0.5) %>% 
  rownames

length(clust1_p)

[1] 6827

#6827 (too many)
length(clust2_p)

[1] 6474

#6474
length(clust3_p)

[1] 607

#607

mf1_genes_p <- clust1_p
mf2_genes_p <- clust2_p
mf3_genes_p <- clust3_p

vennCor <- list(mf1_genes_p, mf2_genes_p, mf3_genes_p)
ggVennDiagram(
  vennCor,
  category.names = c("Motif 1", "Motif 2", "Motif 3")
) + ggtitle("Cormotif Specific and Shared DEGs clustlike")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Extract gene probabilities-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###Use Clustlike and P.post together for Cormotif

#begin with the clustlike cutoffs and then overlay the p.post to check if the genes are present in both

#these filters are the combination of the above analysis to get a gene set that fits in both p.post and clustlike

####motif 1####
#filter 1: clustlike
clust1_genes <- motif_prob %>%
  as.data.frame() %>%
  filter(V1>0.5 & V2<0.5 & V3<0.5) %>% 
  rownames
### Filter 2: Gene-level posterior pattern
prob_filtered_genes_1 <- rownames(gene_prob_all[(gene_prob_all[,1] >0.05 & gene_prob_all[,1] <0.3 & gene_prob_all[,2] <0.5 & gene_prob_all[,3] <0.5),])
### Final intersection of both filters
final_genes_1 <- intersect(clust1_genes, prob_filtered_genes_1)
cat("Number of genes passing both filters:", length(final_genes_1), "\n")

Number of genes passing both filters: 5638 

#5638 genes pass both filters here

####motif 2####
#filter 1: clustlike
clust2_genes <- motif_prob %>%
  as.data.frame() %>%
  filter(V2>0.5 & V1<0.5 & V3<0.5) %>% 
  rownames
### Filter 2: Gene-level posterior pattern
prob_filtered_genes_2 <- rownames(gene_prob_all[(gene_prob_all[,1] >0.5 & gene_prob_all[,2] <0.5 & gene_prob_all[,3] <0.5),])
### Final intersection of both filters
final_genes_2 <- intersect(clust2_genes, prob_filtered_genes_2)
cat("Number of genes passing both filters:", length(final_genes_2), "\n")

Number of genes passing both filters: 6218 

#6218 genes pass both filters here


####motif3####
#filter 1: clustlike
clust3_genes <- motif_prob %>%
  as.data.frame() %>%
  filter(V3 > 0.5 & V1 < 0.5 & V2 < 0.5) %>%
  rownames()
### Filter 2: Gene-level posterior pattern (Motif 2 & 3 high, Motif 1 intermediate)
prob_filtered_genes <- rownames(gene_prob_all[
  gene_prob_all[,1] > 0.3 & gene_prob_all[,1] < 0.9 &
  gene_prob_all[,2] > 0.5 &
  gene_prob_all[,3] > 0.5, ])
### Final intersection of both filters
final_genes_3 <- intersect(clust3_genes, prob_filtered_genes)
cat("Number of genes passing both filters:", length(final_genes_3), "\n")

Number of genes passing both filters: 231 

#231 genes pass both filters here

#what is the proportion of my genes that are included?
5638+6218+231

[1] 12087

#12087
(12087/14319)*100

[1] 84.41232

#84.4% of my genes are represented here out of the 14319 original

#want to find out which genes are not assigned to motifs

final_genes_list <- union(final_genes_1, union(final_genes_2, final_genes_3))
length(final_genes_list)

[1] 12087

#12087 genes as found above
initial_genes_list <- rownames(filcpm_matrix)
length(initial_genes_list)

[1] 14319

#14319 genes as usual
unassigned_genes_list <- setdiff(initial_genes_list, final_genes_list)
length(unassigned_genes_list)

[1] 2232

#2232 genes not assigned - correct number

#saveRDS(unassigned_genes_list, "data/new/Cormotif/unassigned_genes_Cormotif.RDS")

#now, ensure that none of these genes are shared amongst categories
vennCor_final <- list(final_genes_1, final_genes_2, final_genes_3)
ggVennDiagram(
  vennCor_final,
  category.names = c("Motif 1", "Motif 2", "Motif 3")
) + ggtitle("Cormotif Specific and Shared DEGs clustlike + p.post")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Extract Gene Probability clust then p.post-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#no overlapping genes found in these gene sets

clusterdata_dxr_fin <- data.frame(
  Category = c("Motif 1", "Motif 2", "Motif 3"), 
  Value = c(length(final_genes_1), length(final_genes_2), length(final_genes_3))
)

piecolors_dxr_fin <- c("Motif 1" = "#007896", 
                       "Motif 2" = "#58508D",
                       "Motif 3" = "#BC5090")

#make a piechart of these distributions
clusterdata_dxr_fin %>% ggplot(aes(x = "", y = Value, fill = Category))+
  geom_bar(width = 1, stat = "identity")+
  coord_polar("y", start = 0)+
  geom_text(aes(label = Value),
            position = position_stack(vjust = 0.5),
            size = 4, color = "black")+
  labs(title = "Distribution of Gene Clusters Identified By Cormotif", x = NULL, y = NULL)+
  theme_void()+
  scale_fill_manual(values = piecolors_dxr_fin)

Past versions of "Extract Gene Probability clust then p.post-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now, continue by plotting the logFC of all of these gene sets per motif, as well as look at some random genes for log2cpm to see if the patterns are reflected in the example genes

###Plot logFC of Clustlike vs P.post Cormotif

####clustlike logFC of initial set####
##motif 1
length(mf1_genes_p)

[1] 6827

##motif 2 
length(mf2_genes_p)

[1] 6474

##motif 3
length(mf3_genes_p)

[1] 607

#Combine the toptables I have from pairwise analysis into a single dataframe
d24_toptable_dxr <- Toptable_V.D24T %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24")

d24r_toptable_dxr <- Toptable_V.D24R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24R")

d144r_toptable_dxr <- Toptable_V.D144R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "144R")

combined_toptables_dxr <- bind_rows(
  d24_toptable_dxr,
  d24r_toptable_dxr,
  d144r_toptable_dxr)

#Filter the data based on each motif
filt_toptable_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% mf1_genes_p) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 1 (n=6827)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 2 (n=6218)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 3
filt_toptable_3_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_3) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 3 (n=231)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#plots
filt_toptable_dxr_fin

Past versions of "logFC of Clustlike vs P.post Cormotif-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_2_dxr_fin 

Past versions of "logFC of Clustlike vs P.post Cormotif-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_3_dxr_fin

Past versions of "logFC of Clustlike vs P.post Cormotif-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now plot the abs logFC for each of these too
filt_toptable_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 1 (n=5638)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 2 (n=6218)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_3_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_3) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 3 (n=231)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#plots
filt_toptable_abs_fin

Past versions of "logFC of Clustlike vs P.post Cormotif-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_2_abs_fin

Past versions of "logFC of Clustlike vs P.post Cormotif-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_3_abs_fin

Past versions of "logFC of Clustlike vs P.post Cormotif-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###Plot logFC of All Motifs

##motif 1
motif1_genes_fin <- final_genes_1
length(motif1_genes_fin)

[1] 5638

##motif 2 
motif2_genes_fin <- final_genes_2
length(motif2_genes_fin)

[1] 6218

##motif 3
motif3_genes_fin <- final_genes_3
length(motif3_genes_fin)

[1] 231

#Combine the toptables I have from pairwise analysis into a single dataframe
d24_toptable_dxr <- Toptable_V.D24T %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24")

d24r_toptable_dxr <- Toptable_V.D24R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24R")

d144r_toptable_dxr <- Toptable_V.D144R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "144R")

combined_toptables_dxr <- bind_rows(
  d24_toptable_dxr,
  d24r_toptable_dxr,
  d144r_toptable_dxr)

#Filter the data based on each motif
filt_toptable_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 1 (n=5638)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 2 (n=6218)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 3
filt_toptable_3_dxr_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_3) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC for all genes in Motif 3 (n=231)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#plots
filt_toptable_dxr_fin

Past versions of "logFC of Cormotif Motifs-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_2_dxr_fin 

Past versions of "logFC of Cormotif Motifs-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_3_dxr_fin

Past versions of "logFC of Cormotif Motifs-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#now plot the abs logFC for each of these too
filt_toptable_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_1) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 1 (n=5638)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 2 (n=6218)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_3_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_3) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 3 (n=231)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#plots
filt_toptable_abs_fin

Past versions of "logFC of Cormotif Motifs-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_2_abs_fin

Past versions of "logFC of Cormotif Motifs-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

filt_toptable_3_abs_fin

Past versions of "logFC of Cormotif Motifs-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###Put together log2cpm Genes for Each Motif

#use the final genes from cross-verifying with clustlike + p.post

#Load in my count matrices
# final_genes_1
# final_genes_2
# final_genes_3

#these are all the genes that are present in each category, make them into dataframes by filtering out the rest of the genes in my main boxplot df
boxplots_cormotif <- boxplot1

motif1_genes_fin <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% final_genes_1,]
dim(motif1_genes_fin)

[1] 5638   44

#5638 genes in 44 cols
motif2_genes_fin <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% final_genes_2,]
dim(motif2_genes_fin)

[1] 6218   44

#6218 genes in 44 cols
motif3_genes_fin <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% final_genes_3,]
dim(motif3_genes_fin)

[1] 231  44

#231 genes in 44 cols

#pull out some random genes for each using sample

m1_genes_fin <- motif1_genes_fin[sample(nrow(motif1_genes_fin), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes1_fin <- c(m1_genes_fin$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_data_1_fin <- function(gene) {
  gene_data <- motif1_genes_fin %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes1_fin) {
  gene_data <- process_gene_data_1_fin(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression of", gene, "Motif 1")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Cormotif Genes-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####motif 2#####

m2_genes_fin <- motif2_genes_fin[sample(nrow(motif2_genes_fin), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes2_fin <- c(m2_genes_fin$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_datam2_fin <- function(gene) {
  gene_data <- motif2_genes_fin %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#this function is saved under process_gene_data so I will save as an R object

#saveRDS(process_gene_data, "data/new/process_gene_data_funct.RDS")

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes2_fin) {
  gene_data <- process_gene_datam2_fin(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression of", gene, "Motif 2")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Cormotif Genes-4.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####motif 3#####

m3_genes_fin <- motif3_genes_fin[sample(nrow(motif3_genes_fin), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m3_genes
initial_test_genes3_fin <- c(m3_genes_fin$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_datam3_fin <- function(gene) {
  gene_data <- motif3_genes_fin %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes3_fin) {
  gene_data <- process_gene_datam3_fin(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression of", gene, "Motif 3")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Cormotif Genes-7.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Past versions of "log2cpm Cormotif Genes-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###GO/KEGG Final Genes Cormotif

#now take these final gene sets for each motif - clustlike + p.post consensus genes

# final_genes_1
# final_genes_2
# final_genes_3

library(gprofiler2)
#####Motif 1 Gene Set#####
# motif1_genes_matrix <- as.matrix(final_genes_1) 
# colnames(motif1_genes_matrix) <- c("entrezgene_ID")

# saveRDS(motif1_genes_matrix, "data/new/motif1_genes_matrix.RDS")

motif1_genes_matrix <- readRDS("data/new/motif1_genes_matrix.RDS")
length(motif1_genes_matrix)

[1] 5638

#5638 genes in this set for motif 1

motif1_mat_GOKEGG <- gost(query = motif1_genes_matrix,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif1_GOKEGG_genes <- gostplot(motif1_mat_GOKEGG, capped = FALSE, interactive = TRUE)
motif1_GOKEGG_genes

table_motif1_GOKEGG_genes <- motif1_mat_GOKEGG$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif1_GOKEGG_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0019538	protein metabolic process	1530	4721	5.534e-67
GO:BP	GO:0080090	regulation of primary metabolic process	1663	5390	3.258e-57
GO:BP	GO:0046907	intracellular transport	559	1381	2.736e-50
GO:BP	GO:0051179	localization	1668	5555	1.485e-48
GO:BP	GO:0006810	transport	1376	4407	1.007e-47
GO:BP	GO:0051649	establishment of localization in cell	732	2010	1.114e-46
GO:BP	GO:0051641	cellular localization	1179	3661	1.114e-46
GO:BP	GO:0043412	macromolecule modification	1004	3030	2.043e-44
GO:BP	GO:0009056	catabolic process	896	2639	1.174e-43
GO:BP	GO:0006996	organelle organization	1146	3594	8.587e-43
GO:BP	GO:0009057	macromolecule catabolic process	547	1417	3.742e-42
GO:BP	GO:0036211	protein modification process	940	2846	1.631e-40
GO:BP	GO:0048518	positive regulation of biological process	1802	6264	2.887e-40
GO:BP	GO:0048522	positive regulation of cellular process	1717	5920	5.625e-40
GO:BP	GO:0071705	nitrogen compound transport	682	1923	7.303e-39
GO:BP	GO:0033036	macromolecule localization	1034	3228	8.231e-39
GO:BP	GO:0008104	protein localization	907	2770	2.723e-37
GO:BP	GO:0051234	establishment of localization	1460	4928	2.723e-37
GO:BP	GO:0065007	biological regulation	3264	12743	5.102e-37
GO:BP	GO:0070727	cellular macromolecule localization	909	2782	5.102e-37
GO:BP	GO:0015031	protein transport	539	1444	7.520e-37
GO:BP	GO:0030163	protein catabolic process	411	1030	7.217e-35
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	1208	3990	9.411e-34
GO:BP	GO:0050789	regulation of biological process	3152	12336	1.383e-32
GO:BP	GO:0051246	regulation of protein metabolic process	632	1855	6.070e-30
GO:BP	GO:0050794	regulation of cellular process	3051	11946	7.799e-30
GO:BP	GO:0051252	regulation of RNA metabolic process	1112	3687	1.116e-29
GO:BP	GO:0023051	regulation of signaling	1057	3478	2.621e-29
GO:BP	GO:0019222	regulation of metabolic process	1925	7035	7.415e-29
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	320	786	1.349e-28
GO:BP	GO:0010646	regulation of cell communication	1055	3486	1.735e-28
GO:BP	GO:0009966	regulation of signal transduction	938	3034	2.826e-28
GO:BP	GO:0035556	intracellular signal transduction	919	2965	4.949e-28
GO:BP	GO:0048583	regulation of response to stimulus	1180	3993	7.051e-28
GO:BP	GO:0009893	positive regulation of metabolic process	1075	3597	7.801e-27
GO:BP	GO:0032446	protein modification by small protein conjugation	332	853	1.464e-25
GO:BP	GO:0033554	cellular response to stress	608	1830	1.673e-25
GO:BP	GO:0006886	intracellular protein transport	281	686	1.736e-25
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	989	3288	2.466e-25
GO:BP	GO:0006351	DNA-templated transcription	1055	3549	2.639e-25
GO:BP	GO:0016192	vesicle-mediated transport	542	1592	2.707e-25
GO:BP	GO:0043687	post-translational protein modification	382	1027	3.545e-25
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	366	975	6.494e-25
GO:BP	GO:2001141	regulation of RNA biosynthetic process	1021	3428	1.141e-24
GO:BP	GO:0006355	regulation of DNA-templated transcription	1015	3409	1.926e-24
GO:BP	GO:0009894	regulation of catabolic process	383	1040	2.572e-24
GO:BP	GO:0045184	establishment of protein localization	629	1937	1.233e-23
GO:BP	GO:0006796	phosphate-containing compound metabolic process	753	2407	1.472e-23
GO:BP	GO:0006793	phosphorus metabolic process	753	2410	2.126e-23
GO:BP	GO:0051128	regulation of cellular component organization	759	2433	2.126e-23
GO:BP	GO:0016567	protein ubiquitination	300	768	2.274e-23
GO:BP	GO:0007275	multicellular organism development	1335	4727	4.486e-23
GO:BP	GO:1902531	regulation of intracellular signal transduction	630	1953	6.777e-23
GO:BP	GO:0060255	regulation of macromolecule metabolic process	1757	6492	1.313e-22
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	255	628	1.754e-22
GO:BP	GO:0019941	modification-dependent protein catabolic process	257	638	4.424e-22
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	258	643	6.896e-22
GO:BP	GO:0032502	developmental process	1762	6553	3.521e-21
GO:BP	GO:0010498	proteasomal protein catabolic process	225	543	4.552e-21
GO:BP	GO:0048731	system development	1157	4053	5.120e-21
GO:BP	GO:0048856	anatomical structure development	1626	5997	1.318e-20
GO:BP	GO:0065008	regulation of biological quality	876	2947	2.560e-20
GO:BP	GO:0006508	proteolysis	487	1486	9.924e-19
GO:BP	GO:0048585	negative regulation of response to stimulus	538	1680	1.784e-18
GO:BP	GO:0048519	negative regulation of biological process	1572	5834	2.263e-18
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	629	2036	7.568e-18
GO:BP	GO:0009968	negative regulation of signal transduction	439	1326	1.258e-17
GO:BP	GO:0007005	mitochondrion organization	182	435	1.998e-17
GO:BP	GO:0007399	nervous system development	773	2604	2.204e-17
GO:BP	GO:0141124	intracellular signaling cassette	594	1912	2.472e-17
GO:BP	GO:0006366	transcription by RNA polymerase II	799	2711	3.596e-17
GO:BP	GO:0048523	negative regulation of cellular process	1514	5629	4.185e-17
GO:BP	GO:0006915	apoptotic process	595	1923	5.906e-17
GO:BP	GO:0008219	cell death	612	1991	8.342e-17
GO:BP	GO:0006412	translation	268	727	8.342e-17
GO:BP	GO:0012501	programmed cell death	610	1987	1.280e-16
GO:BP	GO:0023057	negative regulation of signaling	464	1435	1.333e-16
GO:BP	GO:0010648	negative regulation of cell communication	464	1436	1.522e-16
GO:BP	GO:0006914	autophagy	228	597	3.069e-16
GO:BP	GO:0061919	process utilizing autophagic mechanism	228	597	3.069e-16
GO:BP	GO:0006950	response to stress	1097	3948	1.435e-15
GO:BP	GO:0032879	regulation of localization	615	2029	1.810e-15
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	754	2578	3.323e-15
GO:BP	GO:0002181	cytoplasmic translation	87	165	3.824e-15
GO:BP	GO:0009891	positive regulation of biosynthetic process	783	2696	4.504e-15
GO:BP	GO:0044238	primary metabolic process	3034	12342	8.204e-15
GO:BP	GO:0051130	positive regulation of cellular component organization	366	1105	1.400e-14
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	754	2593	1.443e-14
GO:BP	GO:0031399	regulation of protein modification process	349	1049	3.584e-14
GO:BP	GO:0051248	negative regulation of protein metabolic process	244	677	6.161e-14
GO:BP	GO:0060341	regulation of cellular localization	338	1013	6.722e-14
GO:BP	GO:0051247	positive regulation of protein metabolic process	345	1039	7.145e-14
GO:BP	GO:0009889	regulation of biosynthetic process	1531	5809	9.620e-14
GO:BP	GO:0050793	regulation of developmental process	714	2457	1.252e-13
GO:BP	GO:0051254	positive regulation of RNA metabolic process	555	1835	1.252e-13
GO:BP	GO:0016236	macroautophagy	149	362	1.600e-13
GO:BP	GO:0016197	endosomal transport	126	290	1.958e-13
GO:BP	GO:0048584	positive regulation of response to stimulus	680	2331	2.795e-13
GO:BP	GO:0033365	protein localization to organelle	388	1209	3.515e-13
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	164	414	3.652e-13
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1487	5644	3.673e-13
GO:BP	GO:0016310	phosphorylation	417	1320	4.750e-13
GO:BP	GO:0048193	Golgi vesicle transport	132	312	4.981e-13
GO:BP	GO:0032880	regulation of protein localization	305	907	5.496e-13
GO:BP	GO:0023056	positive regulation of signaling	541	1796	6.337e-13
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	98	209	7.318e-13
GO:BP	GO:0065009	regulation of molecular function	462	1496	9.281e-13
GO:BP	GO:0009719	response to endogenous stimulus	459	1489	1.584e-12
GO:BP	GO:0010647	positive regulation of cell communication	538	1795	2.000e-12
GO:BP	GO:0080135	regulation of cellular response to stress	193	519	2.041e-12
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	234	662	2.374e-12
GO:BP	GO:0051716	cellular response to stimulus	1886	7376	2.391e-12
GO:BP	GO:0009967	positive regulation of signal transduction	481	1578	2.697e-12
GO:BP	GO:0022008	neurogenesis	531	1771	2.707e-12
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	483	1588	3.454e-12
GO:BP	GO:0044087	regulation of cellular component biogenesis	330	1011	3.454e-12
GO:BP	GO:0009896	positive regulation of catabolic process	200	546	3.617e-12
GO:BP	GO:0042254	ribosome biogenesis	133	323	4.207e-12
GO:BP	GO:0034976	response to endoplasmic reticulum stress	116	270	5.421e-12
GO:BP	GO:0048468	cell development	808	2876	5.534e-12
GO:BP	GO:0030030	cell projection organization	493	1631	5.545e-12
GO:BP	GO:0010468	regulation of gene expression	1450	5536	7.571e-12
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	465	1529	1.058e-11
GO:BP	GO:0042176	regulation of protein catabolic process	146	369	1.089e-11
GO:BP	GO:0090407	organophosphate biosynthetic process	219	619	1.314e-11
GO:BP	GO:0071495	cellular response to endogenous stimulus	384	1223	1.377e-11
GO:BP	GO:0006468	protein phosphorylation	385	1227	1.408e-11
GO:BP	GO:0051253	negative regulation of RNA metabolic process	430	1400	1.844e-11
GO:BP	GO:0019637	organophosphate metabolic process	344	1077	2.300e-11
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	507	1699	2.392e-11
GO:BP	GO:0071840	cellular component organization or biogenesis	2111	8393	2.472e-11
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	506	1697	2.887e-11
GO:BP	GO:0042981	regulation of apoptotic process	445	1462	3.049e-11
GO:BP	GO:1901698	response to nitrogen compound	344	1080	3.335e-11
GO:BP	GO:0043067	regulation of programmed cell death	456	1506	3.664e-11
GO:BP	GO:0000209	protein polyubiquitination	117	280	3.726e-11
GO:BP	GO:0006974	DNA damage response	297	908	4.518e-11
GO:BP	GO:0051049	regulation of transport	481	1607	5.892e-11
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	351	1113	7.941e-11
GO:BP	GO:0044281	small molecule metabolic process	523	1776	1.039e-10
GO:BP	GO:0030154	cell differentiation	1178	4437	1.092e-10
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	312	970	1.120e-10
GO:BP	GO:0048869	cellular developmental process	1178	4438	1.152e-10
GO:BP	GO:0050896	response to stimulus	2243	8999	1.155e-10
GO:BP	GO:1901135	carbohydrate derivative metabolic process	315	983	1.419e-10
GO:BP	GO:0031647	regulation of protein stability	132	335	1.959e-10
GO:BP	GO:0080134	regulation of response to stress	421	1387	1.992e-10
GO:BP	GO:0070925	organelle assembly	331	1046	2.156e-10
GO:BP	GO:0033043	regulation of organelle organization	357	1148	3.608e-10
GO:BP	GO:0034504	protein localization to nucleus	126	318	3.811e-10
GO:BP	GO:0061024	membrane organization	269	821	4.339e-10
GO:BP	GO:0048699	generation of neurons	457	1536	5.774e-10
GO:BP	GO:0009653	anatomical structure morphogenesis	753	2713	6.013e-10
GO:BP	GO:0006417	regulation of translation	144	380	6.102e-10
GO:BP	GO:0051169	nuclear transport	130	334	7.349e-10
GO:BP	GO:0006913	nucleocytoplasmic transport	130	334	7.349e-10
GO:BP	GO:0010970	transport along microtubule	81	178	7.371e-10
GO:BP	GO:0030182	neuron differentiation	434	1451	8.690e-10
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	227	673	8.923e-10
GO:BP	GO:0010256	endomembrane system organization	210	613	1.065e-09
GO:BP	GO:0071363	cellular response to growth factor stimulus	231	689	1.128e-09
GO:BP	GO:0007010	cytoskeleton organization	453	1529	1.332e-09
GO:BP	GO:0099111	microtubule-based transport	94	220	1.366e-09
GO:BP	GO:0010506	regulation of autophagy	139	367	1.373e-09
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	100	239	1.373e-09
GO:BP	GO:0009987	cellular process	4645	20247	1.467e-09
GO:BP	GO:0070848	response to growth factor	239	721	1.721e-09
GO:BP	GO:0030029	actin filament-based process	267	825	2.039e-09
GO:BP	GO:1901873	regulation of post-translational protein modification	101	244	2.261e-09
GO:BP	GO:0030334	regulation of cell migration	303	960	2.288e-09
GO:BP	GO:0051650	establishment of vesicle localization	87	200	2.317e-09
GO:BP	GO:0031344	regulation of cell projection organization	221	658	2.428e-09
GO:BP	GO:0048666	neuron development	360	1177	2.610e-09
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	391	1296	2.636e-09
GO:BP	GO:0051094	positive regulation of developmental process	403	1343	2.844e-09
GO:BP	GO:0007049	cell cycle	485	1663	3.017e-09
GO:BP	GO:0031175	neuron projection development	319	1023	3.142e-09
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	216	642	3.278e-09
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	98	236	3.354e-09
GO:BP	GO:0006753	nucleoside phosphate metabolic process	217	646	3.448e-09
GO:BP	GO:0030162	regulation of proteolysis	149	406	3.628e-09
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	386	1280	3.628e-09
GO:BP	GO:0043069	negative regulation of programmed cell death	287	905	4.067e-09
GO:BP	GO:2000145	regulation of cell motility	318	1022	4.277e-09
GO:BP	GO:0043254	regulation of protein-containing complex assembly	153	421	4.581e-09
GO:BP	GO:0048513	animal organ development	837	3085	4.755e-09
GO:BP	GO:0030036	actin cytoskeleton organization	239	729	5.152e-09
GO:BP	GO:0097190	apoptotic signaling pathway	205	606	5.652e-09
GO:BP	GO:0051648	vesicle localization	92	219	5.797e-09
GO:BP	GO:0031396	regulation of protein ubiquitination	85	197	5.797e-09
GO:BP	GO:0050790	regulation of catalytic activity	292	928	6.818e-09
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	71	155	7.717e-09
GO:BP	GO:0043066	negative regulation of apoptotic process	277	874	9.013e-09
GO:BP	GO:0016477	cell migration	449	1534	9.035e-09
GO:BP	GO:0040012	regulation of locomotion	328	1067	9.549e-09
GO:BP	GO:0036503	ERAD pathway	55	109	1.001e-08
GO:BP	GO:0031346	positive regulation of cell projection organization	133	357	1.129e-08
GO:BP	GO:0034330	cell junction organization	265	834	1.672e-08
GO:BP	GO:0009725	response to hormone	284	907	2.096e-08
GO:BP	GO:0009628	response to abiotic stimulus	346	1144	2.398e-08
GO:BP	GO:0016241	regulation of macroautophagy	79	184	3.291e-08
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	83	197	3.719e-08
GO:BP	GO:0035966	response to topologically incorrect protein	70	157	4.263e-08
GO:BP	GO:0016043	cellular component organization	2028	8184	4.448e-08
GO:BP	GO:0042274	ribosomal small subunit biogenesis	52	104	4.551e-08
GO:BP	GO:0016072	rRNA metabolic process	104	266	4.666e-08
GO:BP	GO:0051640	organelle localization	205	620	4.666e-08
GO:BP	GO:0016032	viral process	150	423	4.666e-08
GO:BP	GO:0097435	supramolecular fiber organization	270	861	4.666e-08
GO:BP	GO:0070887	cellular response to chemical stimulus	609	2192	5.557e-08
GO:BP	GO:0070936	protein K48-linked ubiquitination	50	99	5.944e-08
GO:BP	GO:1903829	positive regulation of protein localization	171	499	6.126e-08
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	127	345	6.385e-08
GO:BP	GO:0006091	generation of precursor metabolites and energy	165	478	6.495e-08
GO:BP	GO:0006364	rRNA processing	91	225	6.825e-08
GO:BP	GO:0006401	RNA catabolic process	118	315	7.309e-08
GO:BP	GO:0007015	actin filament organization	160	461	7.323e-08
GO:BP	GO:0008088	axo-dendritic transport	44	83	7.930e-08
GO:BP	GO:0141188	nucleic acid catabolic process	126	343	8.372e-08
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	180	535	1.084e-07
GO:BP	GO:0006979	response to oxidative stress	142	400	1.123e-07
GO:BP	GO:0051604	protein maturation	181	539	1.143e-07
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	196	594	1.232e-07
GO:BP	GO:0032501	multicellular organismal process	1823	7322	1.565e-07
GO:BP	GO:0007264	small GTPase-mediated signal transduction	171	505	1.575e-07
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	205	629	1.641e-07
GO:BP	GO:0006259	DNA metabolic process	305	1005	1.641e-07
GO:BP	GO:0051656	establishment of organelle localization	167	491	1.652e-07
GO:BP	GO:0006986	response to unfolded protein	63	140	1.672e-07
GO:BP	GO:0051170	import into nucleus	73	171	1.722e-07
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	101	262	1.786e-07
GO:BP	GO:0023052	signaling	1635	6515	1.874e-07
GO:BP	GO:0006839	mitochondrial transport	75	178	2.099e-07
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	116	314	2.364e-07
GO:BP	GO:0006606	protein import into nucleus	71	166	2.492e-07
GO:BP	GO:0031400	negative regulation of protein modification process	126	349	2.632e-07
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	170	505	2.686e-07
GO:BP	GO:0044093	positive regulation of molecular function	272	884	2.749e-07
GO:BP	GO:0007017	microtubule-based process	302	999	2.889e-07
GO:BP	GO:0045862	positive regulation of proteolysis	87	218	2.998e-07
GO:BP	GO:0000902	cell morphogenesis	301	996	3.145e-07
GO:BP	GO:0018193	peptidyl-amino acid modification	219	686	3.191e-07
GO:BP	GO:0009895	negative regulation of catabolic process	129	361	3.476e-07
GO:BP	GO:0045595	regulation of cell differentiation	449	1576	3.603e-07
GO:BP	GO:0045732	positive regulation of protein catabolic process	84	209	3.605e-07
GO:BP	GO:0010975	regulation of neuron projection development	153	446	3.618e-07
GO:BP	GO:0071559	response to transforming growth factor beta	102	269	3.898e-07
GO:BP	GO:0051129	negative regulation of cellular component organization	222	701	5.187e-07
GO:BP	GO:0006897	endocytosis	224	709	5.534e-07
GO:BP	GO:1901700	response to oxygen-containing compound	471	1669	5.618e-07
GO:BP	GO:0007154	cell communication	1635	6540	5.717e-07
GO:BP	GO:0030336	negative regulation of cell migration	108	292	6.825e-07
GO:BP	GO:1901699	cellular response to nitrogen compound	206	645	8.252e-07
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	60	136	8.731e-07
GO:BP	GO:0140694	membraneless organelle assembly	147	430	8.791e-07
GO:BP	GO:0000278	mitotic cell cycle	271	892	1.004e-06
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	255	831	1.004e-06
GO:BP	GO:0051050	positive regulation of transport	259	847	1.095e-06
GO:BP	GO:0072659	protein localization to plasma membrane	107	291	1.107e-06
GO:BP	GO:0072522	purine-containing compound biosynthetic process	97	257	1.111e-06
GO:BP	GO:0001932	regulation of protein phosphorylation	241	779	1.128e-06
GO:BP	GO:0070201	regulation of establishment of protein localization	176	537	1.171e-06
GO:BP	GO:0031401	positive regulation of protein modification process	203	637	1.216e-06
GO:BP	GO:0040011	locomotion	364	1255	1.246e-06
GO:BP	GO:1901800	positive regulation of proteasomal protein catabolic process	52	113	1.316e-06
GO:BP	GO:0042325	regulation of phosphorylation	254	830	1.347e-06
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	82	208	1.384e-06
GO:BP	GO:2001234	negative regulation of apoptotic signaling pathway	89	232	1.662e-06
GO:BP	GO:0032535	regulation of cellular component size	125	356	1.710e-06
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	70	170	1.792e-06
GO:BP	GO:0019220	regulation of phosphate metabolic process	286	956	1.924e-06
GO:BP	GO:0072521	purine-containing compound metabolic process	182	563	1.994e-06
GO:BP	GO:2000146	negative regulation of cell motility	111	308	2.013e-06
GO:BP	GO:0051174	regulation of phosphorus metabolic process	286	957	2.117e-06
GO:BP	GO:0006325	chromatin organization	267	884	2.129e-06
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	281	938	2.164e-06
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	362	1256	2.706e-06
GO:BP	GO:0051239	regulation of multicellular organismal process	781	2956	2.709e-06
GO:BP	GO:0022402	cell cycle process	368	1280	2.766e-06
GO:BP	GO:0010638	positive regulation of organelle organization	162	492	2.766e-06
GO:BP	GO:0009117	nucleotide metabolic process	162	493	3.197e-06
GO:BP	GO:0048870	cell motility	496	1793	3.321e-06
GO:BP	GO:0032870	cellular response to hormone stimulus	201	638	3.442e-06
GO:BP	GO:0032386	regulation of intracellular transport	98	266	3.442e-06
GO:BP	GO:0072359	circulatory system development	333	1145	3.445e-06
GO:BP	GO:0060627	regulation of vesicle-mediated transport	172	531	3.790e-06
GO:BP	GO:0045727	positive regulation of translation	59	138	3.959e-06
GO:BP	GO:0040013	negative regulation of locomotion	115	326	4.139e-06
GO:BP	GO:1990778	protein localization to cell periphery	126	365	4.223e-06
GO:BP	GO:0008654	phospholipid biosynthetic process	95	257	4.390e-06
GO:BP	GO:0006893	Golgi to plasma membrane transport	35	67	4.473e-06
GO:BP	GO:0031334	positive regulation of protein-containing complex assembly	78	201	5.890e-06
GO:BP	GO:0008152	metabolic process	3338	14136	6.117e-06
GO:BP	GO:0035295	tube development	320	1101	6.440e-06
GO:BP	GO:0098657	import into cell	274	922	6.481e-06
GO:BP	GO:0000423	mitophagy	36	71	7.744e-06
GO:BP	GO:0051054	positive regulation of DNA metabolic process	104	291	7.744e-06
GO:BP	GO:1903311	regulation of mRNA metabolic process	110	312	7.744e-06
GO:BP	GO:0071806	protein transmembrane transport	37	74	8.286e-06
GO:BP	GO:0051017	actin filament bundle assembly	65	160	8.726e-06
GO:BP	GO:0016482	cytosolic transport	59	141	9.299e-06
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	50	113	9.681e-06
GO:BP	GO:0030031	cell projection assembly	192	613	9.878e-06
GO:BP	GO:0042592	homeostatic process	478	1736	9.933e-06
GO:BP	GO:0062197	cellular response to chemical stress	111	317	9.933e-06
GO:BP	GO:0031122	cytoplasmic microtubule organization	34	66	9.971e-06
GO:BP	GO:0051338	regulation of transferase activity	161	498	1.031e-05
GO:BP	GO:0032869	cellular response to insulin stimulus	79	207	1.049e-05
GO:BP	GO:0007166	cell surface receptor signaling pathway	742	2819	1.061e-05
GO:BP	GO:0098930	axonal transport	35	69	1.074e-05
GO:BP	GO:0050821	protein stabilization	84	224	1.074e-05
GO:BP	GO:0001944	vasculature development	231	762	1.099e-05
GO:BP	GO:0008283	cell population proliferation	546	2015	1.205e-05
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	188	600	1.231e-05
GO:BP	GO:0006338	chromatin remodeling	221	725	1.245e-05
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	110	315	1.265e-05
GO:BP	GO:0050808	synapse organization	178	563	1.291e-05
GO:BP	GO:0090066	regulation of anatomical structure size	161	500	1.318e-05
GO:BP	GO:0016050	vesicle organization	127	376	1.337e-05
GO:BP	GO:1903321	negative regulation of protein modification by small protein conjugation or removal	42	90	1.397e-05
GO:BP	GO:0009165	nucleotide biosynthetic process	85	229	1.471e-05
GO:BP	GO:0010821	regulation of mitochondrion organization	50	115	1.750e-05
GO:BP	GO:0061572	actin filament bundle organization	65	163	1.800e-05
GO:BP	GO:0043434	response to peptide hormone	144	440	1.868e-05
GO:BP	GO:0046390	ribose phosphate biosynthetic process	71	183	1.889e-05
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	46	103	1.923e-05
GO:BP	GO:1901874	negative regulation of post-translational protein modification	43	94	1.985e-05
GO:BP	GO:1901701	cellular response to oxygen-containing compound	337	1182	2.069e-05
GO:BP	GO:0051052	regulation of DNA metabolic process	160	500	2.124e-05
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	341	1199	2.273e-05
GO:BP	GO:0007006	mitochondrial membrane organization	50	116	2.339e-05
GO:BP	GO:0044092	negative regulation of molecular function	174	553	2.347e-05
GO:BP	GO:0045333	cellular respiration	88	242	2.498e-05
GO:BP	GO:1990542	mitochondrial transmembrane transport	44	98	2.742e-05
GO:BP	GO:0051336	regulation of hydrolase activity	119	352	2.778e-05
GO:BP	GO:0032456	endocytic recycling	40	86	2.779e-05
GO:BP	GO:0016055	Wnt signaling pathway	148	458	2.889e-05
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	206	676	2.959e-05
GO:BP	GO:0042255	ribosome assembly	32	63	3.028e-05
GO:BP	GO:0009060	aerobic respiration	75	199	3.304e-05
GO:BP	GO:0048858	cell projection morphogenesis	207	681	3.356e-05
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	54	130	3.419e-05
GO:BP	GO:0000226	microtubule cytoskeleton organization	204	670	3.510e-05
GO:BP	GO:0000422	autophagy of mitochondrion	46	105	3.560e-05
GO:BP	GO:0009260	ribonucleotide biosynthetic process	68	176	3.649e-05
GO:BP	GO:0008286	insulin receptor signaling pathway	52	124	3.760e-05
GO:BP	GO:1904951	positive regulation of establishment of protein localization	112	329	3.810e-05
GO:BP	GO:0006164	purine nucleotide biosynthetic process	73	193	3.824e-05
GO:BP	GO:0051726	regulation of cell cycle	311	1087	3.830e-05
GO:BP	GO:0007163	establishment or maintenance of cell polarity	85	234	3.830e-05
GO:BP	GO:0051223	regulation of protein transport	143	442	3.916e-05
GO:BP	GO:0007165	signal transduction	1486	6002	3.927e-05
GO:BP	GO:0019693	ribose phosphate metabolic process	126	380	4.014e-05
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	126	380	4.014e-05
GO:BP	GO:0060322	head development	239	806	4.014e-05
GO:BP	GO:0070482	response to oxygen levels	116	344	4.122e-05
GO:BP	GO:1903047	mitotic cell cycle process	223	745	4.297e-05
GO:BP	GO:0019080	viral gene expression	47	109	4.557e-05
GO:BP	GO:0030335	positive regulation of cell migration	174	559	4.628e-05
GO:BP	GO:0009100	glycoprotein metabolic process	123	371	5.307e-05
GO:BP	GO:0035239	tube morphogenesis	257	879	5.335e-05
GO:BP	GO:0001568	blood vessel development	219	732	5.472e-05
GO:BP	GO:0006163	purine nucleotide metabolic process	139	430	5.587e-05
GO:BP	GO:0098927	vesicle-mediated transport between endosomal compartments	26	48	6.131e-05
GO:BP	GO:0051668	localization within membrane	268	924	6.389e-05
GO:BP	GO:0061951	establishment of protein localization to plasma membrane	32	65	6.792e-05
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	55	136	6.917e-05
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	105	308	7.097e-05
GO:BP	GO:0030522	intracellular receptor signaling pathway	124	377	7.385e-05
GO:BP	GO:0045786	negative regulation of cell cycle	124	377	7.385e-05
GO:BP	GO:0034329	cell junction assembly	158	503	7.507e-05
GO:BP	GO:0006403	RNA localization	74	200	7.905e-05
GO:BP	GO:0006281	DNA repair	189	621	8.209e-05
GO:BP	GO:0009142	nucleoside triphosphate biosynthetic process	52	127	8.214e-05
GO:BP	GO:2000147	positive regulation of cell motility	180	587	8.399e-05
GO:BP	GO:0043542	endothelial cell migration	80	221	8.448e-05
GO:BP	GO:0075522	IRES-dependent viral translational initiation	10	11	9.040e-05
GO:BP	GO:2000026	regulation of multicellular organismal development	391	1418	9.146e-05
GO:BP	GO:0007033	vacuole organization	85	239	9.454e-05
GO:BP	GO:0043085	positive regulation of catalytic activity	171	554	9.454e-05
GO:BP	GO:0019058	viral life cycle	105	310	9.562e-05
GO:BP	GO:2000781	positive regulation of double-strand break repair	41	93	9.947e-05
GO:BP	GO:0009259	ribonucleotide metabolic process	122	372	1.007e-04
GO:BP	GO:0000266	mitochondrial fission	23	41	1.017e-04
GO:BP	GO:0010508	positive regulation of autophagy	62	161	1.078e-04
GO:BP	GO:0009152	purine ribonucleotide biosynthetic process	62	161	1.078e-04
GO:BP	GO:0031648	protein destabilization	27	52	1.084e-04
GO:BP	GO:0006402	mRNA catabolic process	91	261	1.094e-04
GO:BP	GO:0007417	central nervous system development	301	1061	1.112e-04
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	45	106	1.153e-04
GO:BP	GO:0010976	positive regulation of neuron projection development	61	158	1.153e-04
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	114	344	1.175e-04
GO:BP	GO:0000165	MAPK cascade	220	744	1.175e-04
GO:BP	GO:0008610	lipid biosynthetic process	216	729	1.231e-04
GO:BP	GO:0009201	ribonucleoside triphosphate biosynthetic process	49	119	1.233e-04
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	95	276	1.238e-04
GO:BP	GO:0048812	neuron projection morphogenesis	198	660	1.276e-04
GO:BP	GO:0006629	lipid metabolic process	383	1391	1.278e-04
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	89	255	1.290e-04
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	98	287	1.290e-04
GO:BP	GO:0046903	secretion	283	992	1.308e-04
GO:BP	GO:0009888	tissue development	540	2032	1.372e-04
GO:BP	GO:0051258	protein polymerization	97	284	1.411e-04
GO:BP	GO:2000142	regulation of DNA-templated transcription initiation	37	82	1.438e-04
GO:BP	GO:0030111	regulation of Wnt signaling pathway	110	331	1.440e-04
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	34	73	1.443e-04
GO:BP	GO:0043487	regulation of RNA stability	71	193	1.443e-04
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	119	364	1.468e-04
GO:BP	GO:0051896	regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	91	263	1.482e-04
GO:BP	GO:0048514	blood vessel morphogenesis	191	635	1.514e-04
GO:BP	GO:0061061	muscle structure development	206	693	1.552e-04
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	90	260	1.621e-04
GO:BP	GO:0006282	regulation of DNA repair	80	225	1.683e-04
GO:BP	GO:0032388	positive regulation of intracellular transport	55	140	1.736e-04
GO:BP	GO:0006898	receptor-mediated endocytosis	91	264	1.741e-04
GO:BP	GO:0099003	vesicle-mediated transport in synapse	89	257	1.768e-04
GO:BP	GO:0040007	growth	266	929	1.801e-04
GO:BP	GO:0009150	purine ribonucleotide metabolic process	115	351	1.827e-04
GO:BP	GO:0060070	canonical Wnt signaling pathway	104	311	1.830e-04
GO:BP	GO:0045739	positive regulation of DNA repair	54	137	1.844e-04
GO:BP	GO:0007420	brain development	221	754	2.010e-04
GO:BP	GO:0033143	regulation of intracellular steroid hormone receptor signaling pathway	33	71	2.010e-04
GO:BP	GO:0031397	negative regulation of protein ubiquitination	35	77	2.010e-04
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	44	105	2.028e-04
GO:BP	GO:0051222	positive regulation of protein transport	89	258	2.063e-04
GO:BP	GO:0009892	negative regulation of metabolic process	860	3375	2.076e-04
GO:BP	GO:0006754	ATP biosynthetic process	43	102	2.116e-04
GO:BP	GO:0043087	regulation of GTPase activity	73	202	2.116e-04
GO:BP	GO:0015931	nucleobase-containing compound transport	83	237	2.133e-04
GO:BP	GO:0031589	cell-substrate adhesion	116	356	2.161e-04
GO:BP	GO:0043065	positive regulation of apoptotic process	162	528	2.181e-04
GO:BP	GO:0001666	response to hypoxia	101	302	2.380e-04
GO:BP	GO:0072384	organelle transport along microtubule	39	90	2.489e-04
GO:BP	GO:0032868	response to insulin	92	270	2.523e-04
GO:BP	GO:0006399	tRNA metabolic process	75	210	2.560e-04
GO:BP	GO:0001701	in utero embryonic development	131	413	2.634e-04
GO:BP	GO:1901875	positive regulation of post-translational protein modification	52	132	2.649e-04
GO:BP	GO:0001667	ameboidal-type cell migration	82	235	2.758e-04
GO:BP	GO:1900076	regulation of cellular response to insulin stimulus	33	72	2.804e-04
GO:BP	GO:0055085	transmembrane transport	426	1578	2.804e-04
GO:BP	GO:0030010	establishment of cell polarity	60	159	2.804e-04
GO:BP	GO:0040017	positive regulation of locomotion	181	603	2.804e-04
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	89	260	2.804e-04
GO:BP	GO:0042770	signal transduction in response to DNA damage	64	173	3.060e-04
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	106	322	3.067e-04
GO:BP	GO:0009790	embryo development	316	1135	3.073e-04
GO:BP	GO:0001525	angiogenesis	166	547	3.248e-04
GO:BP	GO:0051493	regulation of cytoskeleton organization	158	517	3.422e-04
GO:BP	GO:0034599	cellular response to oxidative stress	85	247	3.425e-04
GO:BP	GO:0051348	negative regulation of transferase activity	62	167	3.604e-04
GO:BP	GO:0006457	protein folding	77	219	3.604e-04
GO:BP	GO:0042177	negative regulation of protein catabolic process	47	117	3.668e-04
GO:BP	GO:0007034	vacuolar transport	64	174	3.693e-04
GO:BP	GO:0045597	positive regulation of cell differentiation	251	879	3.693e-04
GO:BP	GO:0018105	peptidyl-serine phosphorylation	64	174	3.693e-04
GO:BP	GO:0009145	purine nucleoside triphosphate biosynthetic process	46	114	3.883e-04
GO:BP	GO:0072331	signal transduction by p53 class mediator	61	164	3.883e-04
GO:BP	GO:0036010	protein localization to endosome	17	28	3.938e-04
GO:BP	GO:0072594	establishment of protein localization to organelle	195	661	4.086e-04
GO:BP	GO:0032271	regulation of protein polymerization	71	199	4.282e-04
GO:BP	GO:0043068	positive regulation of programmed cell death	165	546	4.317e-04
GO:BP	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	99	299	4.323e-04
GO:BP	GO:1903322	positive regulation of protein modification by small protein conjugation or removal	51	131	4.442e-04
GO:BP	GO:0032527	protein exit from endoplasmic reticulum	24	47	4.495e-04
GO:BP	GO:0050792	regulation of viral process	59	158	4.547e-04
GO:BP	GO:0048661	positive regulation of smooth muscle cell proliferation	37	86	4.714e-04
GO:BP	GO:0048545	response to steroid hormone	110	340	4.756e-04
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	101	307	4.756e-04
GO:BP	GO:0099504	synaptic vesicle cycle	77	221	4.994e-04
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	55	145	5.074e-04
GO:BP	GO:0043086	negative regulation of catalytic activity	97	293	5.158e-04
GO:BP	GO:0051168	nuclear export	62	169	5.262e-04
GO:BP	GO:0060260	regulation of transcription initiation by RNA polymerase II	33	74	5.277e-04
GO:BP	GO:0033157	regulation of intracellular protein transport	57	152	5.311e-04
GO:BP	GO:0061462	protein localization to lysosome	28	59	5.327e-04
GO:BP	GO:1900078	positive regulation of cellular response to insulin stimulus	16	26	5.327e-04
GO:BP	GO:0045017	glycerolipid biosynthetic process	85	250	5.367e-04
GO:BP	GO:0043408	regulation of MAPK cascade	188	637	5.367e-04
GO:BP	GO:0007044	cell-substrate junction assembly	40	96	5.367e-04
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	48	122	5.393e-04
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	54	142	5.393e-04
GO:BP	GO:0010628	positive regulation of gene expression	333	1212	5.453e-04
GO:BP	GO:0046034	ATP metabolic process	79	229	5.700e-04
GO:BP	GO:0045022	early endosome to late endosome transport	22	42	5.708e-04
GO:BP	GO:0036293	response to decreased oxygen levels	103	316	5.876e-04
GO:BP	GO:0034644	cellular response to UV	38	90	5.876e-04
GO:BP	GO:0043484	regulation of RNA splicing	67	187	5.894e-04
GO:BP	GO:0051236	establishment of RNA localization	60	163	6.099e-04
GO:BP	GO:0034063	stress granule assembly	19	34	6.119e-04
GO:BP	GO:1902903	regulation of supramolecular fiber organization	121	383	6.129e-04
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	64	177	6.329e-04
GO:BP	GO:0045859	regulation of protein kinase activity	126	402	6.329e-04
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	64	177	6.329e-04
GO:BP	GO:0019725	cellular homeostasis	238	835	6.389e-04
GO:BP	GO:0061013	regulation of mRNA catabolic process	70	198	6.389e-04
GO:BP	GO:0008154	actin polymerization or depolymerization	68	191	6.389e-04
GO:BP	GO:0021543	pallium development	70	198	6.389e-04
GO:BP	GO:0032970	regulation of actin filament-based process	119	376	6.408e-04
GO:BP	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	45	113	6.447e-04
GO:BP	GO:0007040	lysosome organization	45	113	6.447e-04
GO:BP	GO:0080171	lytic vacuole organization	45	113	6.447e-04
GO:BP	GO:0050658	RNA transport	59	160	6.476e-04
GO:BP	GO:0050657	nucleic acid transport	59	160	6.476e-04
GO:BP	GO:0006623	protein targeting to vacuole	24	48	6.511e-04
GO:BP	GO:0015986	proton motive force-driven ATP synthesis	34	78	6.706e-04
GO:BP	GO:0009615	response to virus	129	414	6.765e-04
GO:BP	GO:0043488	regulation of mRNA stability	65	181	6.821e-04
GO:BP	GO:0048009	insulin-like growth factor receptor signaling pathway	25	51	6.821e-04
GO:BP	GO:2000144	positive regulation of DNA-templated transcription initiation	31	69	7.173e-04
GO:BP	GO:0110053	regulation of actin filament organization	88	263	7.173e-04
GO:BP	GO:0070534	protein K63-linked ubiquitination	31	69	7.173e-04
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	801	3157	7.173e-04
GO:BP	GO:0007041	lysosomal transport	52	137	7.537e-04
GO:BP	GO:0006626	protein targeting to mitochondrion	42	104	7.745e-04
GO:BP	GO:0140053	mitochondrial gene expression	61	168	7.987e-04
GO:BP	GO:0006352	DNA-templated transcription initiation	73	210	7.996e-04
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	85	253	8.119e-04
GO:BP	GO:0006622	protein targeting to lysosome	18	32	8.347e-04
GO:BP	GO:0043549	regulation of kinase activity	133	431	8.347e-04
GO:BP	GO:0005975	carbohydrate metabolic process	167	561	8.415e-04
GO:BP	GO:0071453	cellular response to oxygen levels	60	165	8.659e-04
GO:BP	GO:0042542	response to hydrogen peroxide	40	98	8.695e-04
GO:BP	GO:0019079	viral genome replication	50	131	8.745e-04
GO:BP	GO:0042127	regulation of cell population proliferation	447	1685	8.834e-04
GO:BP	GO:0018209	peptidyl-serine modification	66	186	8.844e-04
GO:BP	GO:0009411	response to UV	57	155	9.168e-04
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	52	138	9.213e-04
GO:BP	GO:0060491	regulation of cell projection assembly	71	204	9.482e-04
GO:BP	GO:0007507	heart development	178	605	9.584e-04
GO:BP	GO:0099518	vesicle cytoskeletal trafficking	29	64	1.011e-03
GO:BP	GO:0000271	polysaccharide biosynthetic process	26	55	1.011e-03
GO:BP	GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process	26	55	1.011e-03
GO:BP	GO:0072665	protein localization to vacuole	37	89	1.019e-03
GO:BP	GO:0033002	muscle cell proliferation	72	208	1.019e-03
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	41	102	1.042e-03
GO:BP	GO:0003174	mitral valve development	10	13	1.047e-03
GO:BP	GO:0009314	response to radiation	134	437	1.049e-03
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	200	692	1.056e-03
GO:BP	GO:0070585	protein localization to mitochondrion	50	132	1.069e-03
GO:BP	GO:0007160	cell-matrix adhesion	80	237	1.079e-03
GO:BP	GO:0006644	phospholipid metabolic process	122	392	1.086e-03
GO:BP	GO:0060537	muscle tissue development	132	430	1.113e-03
GO:BP	GO:0033145	positive regulation of intracellular steroid hormone receptor signaling pathway	9	11	1.113e-03
GO:BP	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	34	80	1.170e-03
GO:BP	GO:0014706	striated muscle tissue development	126	408	1.206e-03
GO:BP	GO:0120032	regulation of plasma membrane bounded cell projection assembly	70	202	1.208e-03
GO:BP	GO:0010586	miRNA metabolic process	42	106	1.233e-03
GO:BP	GO:0009451	RNA modification	62	174	1.239e-03
GO:BP	GO:0051240	positive regulation of multicellular organismal process	441	1667	1.250e-03
GO:BP	GO:2000779	regulation of double-strand break repair	53	143	1.257e-03
GO:BP	GO:0061077	chaperone-mediated protein folding	32	74	1.260e-03
GO:BP	GO:0051345	positive regulation of hydrolase activity	71	206	1.292e-03
GO:BP	GO:0042326	negative regulation of phosphorylation	86	260	1.292e-03
GO:BP	GO:0043009	chordate embryonic development	194	671	1.293e-03
GO:BP	GO:0034446	substrate adhesion-dependent cell spreading	41	103	1.305e-03
GO:BP	GO:0150115	cell-substrate junction organization	41	103	1.305e-03
GO:BP	GO:0000302	response to reactive oxygen species	69	199	1.305e-03
GO:BP	GO:0000723	telomere maintenance	59	164	1.328e-03
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	106	334	1.341e-03
GO:BP	GO:0170036	import into the mitochondrion	24	50	1.367e-03
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	72	210	1.373e-03
GO:BP	GO:0050769	positive regulation of neurogenesis	82	246	1.379e-03
GO:BP	GO:0006383	transcription by RNA polymerase III	28	62	1.381e-03
GO:BP	GO:1901799	negative regulation of proteasomal protein catabolic process	26	56	1.395e-03
GO:BP	GO:0051028	mRNA transport	49	130	1.395e-03
GO:BP	GO:0044770	cell cycle phase transition	158	532	1.403e-03
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	88	268	1.403e-03
GO:BP	GO:0032940	secretion by cell	240	854	1.412e-03
GO:BP	GO:0005977	glycogen metabolic process	35	84	1.427e-03
GO:BP	GO:1901652	response to peptide	267	962	1.427e-03
GO:BP	GO:0030041	actin filament polymerization	58	161	1.427e-03
GO:BP	GO:0043123	positive regulation of canonical NF-kappaB signal transduction	73	214	1.449e-03
GO:BP	GO:0032259	methylation	79	236	1.550e-03
GO:BP	GO:1901798	positive regulation of signal transduction by p53 class mediator	16	28	1.574e-03
GO:BP	GO:1903513	endoplasmic reticulum to cytosol transport	16	28	1.574e-03
GO:BP	GO:0030970	retrograde protein transport, ER to cytosol	16	28	1.574e-03
GO:BP	GO:0000028	ribosomal small subunit assembly	12	18	1.582e-03
GO:BP	GO:0048872	homeostasis of number of cells	105	332	1.632e-03
GO:BP	GO:0140352	export from cell	258	928	1.644e-03
GO:BP	GO:0035357	peroxisome proliferator activated receptor signaling pathway	14	23	1.713e-03
GO:BP	GO:0010594	regulation of endothelial cell migration	60	169	1.713e-03
GO:BP	GO:0016239	positive regulation of macroautophagy	36	88	1.755e-03
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	21	42	1.761e-03
GO:BP	GO:0032101	regulation of response to external stimulus	296	1082	1.784e-03
GO:BP	GO:0006903	vesicle targeting	29	66	1.824e-03
GO:BP	GO:0072666	establishment of protein localization to vacuole	29	66	1.824e-03
GO:BP	GO:0048041	focal adhesion assembly	35	85	1.852e-03
GO:BP	GO:0010257	NADH dehydrogenase complex assembly	28	63	1.864e-03
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	17	31	1.864e-03
GO:BP	GO:0032981	mitochondrial respiratory chain complex I assembly	28	63	1.864e-03
GO:BP	GO:0051962	positive regulation of nervous system development	95	296	1.865e-03
GO:BP	GO:0030038	contractile actin filament bundle assembly	42	108	1.878e-03
GO:BP	GO:0031398	positive regulation of protein ubiquitination	42	108	1.878e-03
GO:BP	GO:0006513	protein monoubiquitination	23	48	1.878e-03
GO:BP	GO:0043149	stress fiber assembly	42	108	1.878e-03
GO:BP	GO:0043547	positive regulation of GTPase activity	50	135	1.884e-03
GO:BP	GO:0071456	cellular response to hypoxia	52	142	1.940e-03
GO:BP	GO:0010948	negative regulation of cell cycle process	93	289	1.948e-03
GO:BP	GO:0001933	negative regulation of protein phosphorylation	81	245	1.950e-03
GO:BP	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	41	105	2.013e-03
GO:BP	GO:0034497	protein localization to phagophore assembly site	11	16	2.017e-03
GO:BP	GO:0017148	negative regulation of translation	49	132	2.040e-03
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	72	213	2.119e-03
GO:BP	GO:0005976	polysaccharide metabolic process	40	102	2.161e-03
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	43	112	2.163e-03
GO:BP	GO:0032204	regulation of telomere maintenance	43	112	2.163e-03
GO:BP	GO:0001934	positive regulation of protein phosphorylation	144	483	2.203e-03
GO:BP	GO:0038127	ERBB signaling pathway	48	129	2.209e-03
GO:BP	GO:0010810	regulation of cell-substrate adhesion	73	217	2.240e-03
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	101	320	2.273e-03
GO:BP	GO:1901524	regulation of mitophagy	19	37	2.288e-03
GO:BP	GO:0071514	genomic imprinting	13	21	2.293e-03
GO:BP	GO:0040008	regulation of growth	175	604	2.319e-03
GO:BP	GO:0044042	glucan metabolic process	35	86	2.341e-03
GO:BP	GO:0048589	developmental growth	190	663	2.341e-03
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	60	171	2.355e-03
GO:BP	GO:0060816	random inactivation of X chromosome	10	14	2.534e-03
GO:BP	GO:0009250	glucan biosynthetic process	21	43	2.555e-03
GO:BP	GO:0005978	glycogen biosynthetic process	21	43	2.555e-03
GO:BP	GO:0008064	regulation of actin polymerization or depolymerization	53	147	2.563e-03
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	46	123	2.581e-03
GO:BP	GO:0034097	response to cytokine	261	947	2.581e-03
GO:BP	GO:0021537	telencephalon development	91	284	2.612e-03
GO:BP	GO:0007155	cell adhesion	404	1530	2.672e-03
GO:BP	GO:0007029	endoplasmic reticulum organization	40	103	2.673e-03
GO:BP	GO:0008637	apoptotic mitochondrial changes	40	103	2.673e-03
GO:BP	GO:0051897	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	64	186	2.687e-03
GO:BP	GO:0003151	outflow tract morphogenesis	32	77	2.759e-03
GO:BP	GO:0048729	tissue morphogenesis	177	614	2.760e-03
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	52	144	2.767e-03
GO:BP	GO:0007266	Rho protein signal transduction	52	144	2.767e-03
GO:BP	GO:0097581	lamellipodium organization	36	90	2.784e-03
GO:BP	GO:0043409	negative regulation of MAPK cascade	56	158	2.791e-03
GO:BP	GO:0051402	neuron apoptotic process	94	296	2.887e-03
GO:BP	GO:0046628	positive regulation of insulin receptor signaling pathway	14	24	2.976e-03
GO:BP	GO:0003183	mitral valve morphogenesis	9	12	3.032e-03
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	96	304	3.070e-03
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	96	304	3.070e-03
GO:BP	GO:0010595	positive regulation of endothelial cell migration	41	107	3.070e-03
GO:BP	GO:0090316	positive regulation of intracellular protein transport	38	97	3.070e-03
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	41	107	3.070e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	206	730	3.096e-03
GO:BP	GO:0001649	osteoblast differentiation	77	234	3.132e-03
GO:BP	GO:0033993	response to lipid	256	930	3.132e-03
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	98	312	3.267e-03
GO:BP	GO:0046854	phosphatidylinositol phosphate biosynthetic process	28	65	3.286e-03
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	40	104	3.291e-03
GO:BP	GO:0002009	morphogenesis of an epithelium	148	503	3.291e-03
GO:BP	GO:0048227	plasma membrane to endosome transport	7	8	3.354e-03
GO:BP	GO:0070427	nucleotide-binding oligomerization domain containing 1 signaling pathway	7	8	3.354e-03
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	45	121	3.358e-03
GO:BP	GO:0033148	positive regulation of intracellular estrogen receptor signaling pathway	8	10	3.379e-03
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	19	38	3.379e-03
GO:BP	GO:0060284	regulation of cell development	235	847	3.391e-03
GO:BP	GO:0043523	regulation of neuron apoptotic process	79	242	3.412e-03
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	61	177	3.441e-03
GO:BP	GO:0030833	regulation of actin filament polymerization	47	128	3.441e-03
GO:BP	GO:0038179	neurotrophin signaling pathway	20	41	3.521e-03
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	51	142	3.556e-03
GO:BP	GO:1903146	regulation of autophagy of mitochondrion	21	44	3.615e-03
GO:BP	GO:0051646	mitochondrion localization	24	53	3.622e-03
GO:BP	GO:0016049	cell growth	143	485	3.698e-03
GO:BP	GO:0014812	muscle cell migration	35	88	3.713e-03
GO:BP	GO:0031929	TOR signaling	58	167	3.817e-03
GO:BP	GO:0021987	cerebral cortex development	48	132	3.817e-03
GO:BP	GO:1900180	regulation of protein localization to nucleus	52	146	3.880e-03
GO:BP	GO:0007030	Golgi organization	54	153	3.880e-03
GO:BP	GO:0048871	multicellular organismal-level homeostasis	229	825	3.880e-03
GO:BP	GO:0050767	regulation of neurogenesis	115	378	3.910e-03
GO:BP	GO:0001952	regulation of cell-matrix adhesion	45	122	4.051e-03
GO:BP	GO:0051091	positive regulation of DNA-binding transcription factor activity	66	196	4.056e-03
GO:BP	GO:0007063	regulation of sister chromatid cohesion	11	17	4.064e-03
GO:BP	GO:0010639	negative regulation of organelle organization	108	352	4.170e-03
GO:BP	GO:0030832	regulation of actin filament length	53	150	4.232e-03
GO:BP	GO:0042327	positive regulation of phosphorylation	148	506	4.244e-03
GO:BP	GO:0070301	cellular response to hydrogen peroxide	28	66	4.288e-03
GO:BP	GO:0009306	protein secretion	115	379	4.331e-03
GO:BP	GO:0001558	regulation of cell growth	122	406	4.428e-03
GO:BP	GO:1905475	regulation of protein localization to membrane	65	193	4.428e-03
GO:BP	GO:0060261	positive regulation of transcription initiation by RNA polymerase II	27	63	4.471e-03
GO:BP	GO:0035967	cellular response to topologically incorrect protein	41	109	4.579e-03
GO:BP	GO:1903828	negative regulation of protein localization	71	215	4.583e-03
GO:BP	GO:0031669	cellular response to nutrient levels	80	248	4.583e-03
GO:BP	GO:0018205	peptidyl-lysine modification	50	140	4.586e-03
GO:BP	GO:0034614	cellular response to reactive oxygen species	52	147	4.586e-03
GO:BP	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	38	99	4.662e-03
GO:BP	GO:0048010	vascular endothelial growth factor receptor signaling pathway	25	57	4.792e-03
GO:BP	GO:0010761	fibroblast migration	24	54	4.930e-03
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	19	39	4.930e-03
GO:BP	GO:0051882	mitochondrial depolarization	14	25	4.932e-03
GO:BP	GO:0032543	mitochondrial translation	47	130	4.949e-03
GO:BP	GO:0006900	vesicle budding from membrane	34	86	4.969e-03
GO:BP	GO:0048013	ephrin receptor signaling pathway	23	51	5.002e-03
GO:BP	GO:0008089	anterograde axonal transport	23	51	5.002e-03
GO:BP	GO:0050803	regulation of synapse structure or activity	98	316	5.018e-03
GO:BP	GO:0006476	protein deacetylation	20	42	5.018e-03
GO:BP	GO:0030900	forebrain development	126	423	5.136e-03
GO:BP	GO:0062012	regulation of small molecule metabolic process	99	320	5.146e-03
GO:BP	GO:0061564	axon development	153	528	5.203e-03
GO:BP	GO:0010720	positive regulation of cell development	135	458	5.234e-03
GO:BP	GO:0042273	ribosomal large subunit biogenesis	29	70	5.263e-03
GO:BP	GO:0032922	circadian regulation of gene expression	29	70	5.263e-03
GO:BP	GO:0050807	regulation of synapse organization	96	309	5.309e-03
GO:BP	GO:0051444	negative regulation of ubiquitin-protein transferase activity	10	15	5.309e-03
GO:BP	GO:0019827	stem cell population maintenance	61	180	5.364e-03
GO:BP	GO:0050684	regulation of mRNA processing	48	134	5.373e-03
GO:BP	GO:0006354	DNA-templated transcription elongation	48	134	5.373e-03
GO:BP	GO:0033044	regulation of chromosome organization	78	242	5.378e-03
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	28	67	5.508e-03
GO:BP	GO:0006517	protein deglycosylation	12	20	5.508e-03
GO:BP	GO:0046626	regulation of insulin receptor signaling pathway	28	67	5.508e-03
GO:BP	GO:0043603	amide metabolic process	134	455	5.620e-03
GO:BP	GO:0035592	establishment of protein localization to extracellular region	115	382	5.752e-03
GO:BP	GO:0033059	cellular pigmentation	27	64	5.794e-03
GO:BP	GO:0031667	response to nutrient levels	148	510	5.881e-03
GO:BP	GO:0046486	glycerolipid metabolic process	119	398	6.146e-03
GO:BP	GO:0030511	positive regulation of transforming growth factor beta receptor signaling pathway	16	31	6.154e-03
GO:BP	GO:0065002	intracellular protein transmembrane transport	16	31	6.154e-03
GO:BP	GO:0046685	response to arsenic-containing substance	16	31	6.154e-03
GO:BP	GO:1903846	positive regulation of cellular response to transforming growth factor beta stimulus	16	31	6.154e-03
GO:BP	GO:0051093	negative regulation of developmental process	252	925	6.163e-03
GO:BP	GO:0002262	myeloid cell homeostasis	61	181	6.182e-03
GO:BP	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	44	121	6.270e-03
GO:BP	GO:0098732	macromolecule deacylation	25	58	6.292e-03
GO:BP	GO:0036294	cellular response to decreased oxygen levels	52	149	6.294e-03
GO:BP	GO:0010934	macrophage cytokine production	18	37	6.848e-03
GO:BP	GO:0060271	cilium assembly	120	403	6.848e-03
GO:BP	GO:0010935	regulation of macrophage cytokine production	18	37	6.848e-03
GO:BP	GO:0006119	oxidative phosphorylation	51	146	6.877e-03
GO:BP	GO:0061082	myeloid leukocyte cytokine production	22	49	6.877e-03
GO:BP	GO:0050770	regulation of axonogenesis	51	146	6.877e-03
GO:BP	GO:0061028	establishment of endothelial barrier	22	49	6.877e-03
GO:BP	GO:0048660	regulation of smooth muscle cell proliferation	49	139	6.925e-03
GO:BP	GO:0007416	synapse assembly	82	259	6.984e-03
GO:BP	GO:0048489	synaptic vesicle transport	20	43	7.005e-03
GO:BP	GO:0071692	protein localization to extracellular region	116	388	7.048e-03
GO:BP	GO:0007517	muscle organ development	110	365	7.054e-03
GO:BP	GO:0043524	negative regulation of neuron apoptotic process	56	164	7.095e-03
GO:BP	GO:0031503	protein-containing complex localization	70	215	7.343e-03
GO:BP	GO:0072657	protein localization to membrane	227	827	7.351e-03
GO:BP	GO:0043473	pigmentation	42	115	7.376e-03
GO:BP	GO:1904294	positive regulation of ERAD pathway	11	18	7.471e-03
GO:BP	GO:0007032	endosome organization	37	98	7.471e-03
GO:BP	GO:2000641	regulation of early endosome to late endosome transport	11	18	7.471e-03
GO:BP	GO:0048659	smooth muscle cell proliferation	50	143	7.471e-03
GO:BP	GO:0001522	pseudouridine synthesis	11	18	7.471e-03
GO:BP	GO:0097494	regulation of vesicle size	11	18	7.471e-03
GO:BP	GO:0006112	energy reserve metabolic process	37	98	7.471e-03
GO:BP	GO:0030099	myeloid cell differentiation	130	443	7.595e-03
GO:BP	GO:0046777	protein autophosphorylation	60	179	7.738e-03
GO:BP	GO:0019081	viral translation	14	26	7.763e-03
GO:BP	GO:0070198	protein localization to chromosome, telomeric region	14	26	7.763e-03
GO:BP	GO:0007549	sex-chromosome dosage compensation	14	26	7.763e-03
GO:BP	GO:0048167	regulation of synaptic plasticity	72	223	7.898e-03
GO:BP	GO:0031032	actomyosin structure organization	69	212	7.934e-03
GO:BP	GO:0034101	erythrocyte homeostasis	51	147	7.974e-03
GO:BP	GO:0045861	negative regulation of proteolysis	51	147	7.974e-03
GO:BP	GO:0042455	ribonucleoside biosynthetic process	8	11	8.519e-03
GO:BP	GO:0046129	purine ribonucleoside biosynthetic process	8	11	8.519e-03
GO:BP	GO:0042451	purine nucleoside biosynthetic process	8	11	8.519e-03
GO:BP	GO:0090140	regulation of mitochondrial fission	15	29	8.565e-03
GO:BP	GO:0090311	regulation of protein deacetylation	15	29	8.565e-03
GO:BP	GO:0035051	cardiocyte differentiation	52	151	8.567e-03
GO:BP	GO:0010657	muscle cell apoptotic process	32	82	8.740e-03
GO:BP	GO:0032200	telomere organization	63	191	9.040e-03
GO:BP	GO:0090559	regulation of membrane permeability	28	69	9.053e-03
GO:BP	GO:0051301	cell division	184	658	9.080e-03
GO:BP	GO:0040029	epigenetic regulation of gene expression	92	299	9.080e-03
GO:BP	GO:0045088	regulation of innate immune response	131	449	9.098e-03
GO:BP	GO:0035601	protein deacylation	22	50	9.205e-03
GO:BP	GO:0098727	maintenance of cell number	61	184	9.366e-03
GO:BP	GO:0050772	positive regulation of axonogenesis	31	79	9.366e-03
GO:BP	GO:0106070	regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	12	21	9.373e-03
GO:BP	GO:0006984	ER-nucleus signaling pathway	21	47	9.432e-03
GO:BP	GO:0043045	epigenetic programming of gene expression	17	35	9.452e-03
GO:BP	GO:0006516	glycoprotein catabolic process	18	38	9.624e-03
GO:BP	GO:0006413	translational initiation	45	127	9.624e-03
GO:BP	GO:0010762	regulation of fibroblast migration	18	38	9.624e-03
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	19	41	9.653e-03
GO:BP	GO:0010660	regulation of muscle cell apoptotic process	30	76	1.002e-02
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	33	86	1.004e-02
GO:BP	GO:0030200	heparan sulfate proteoglycan catabolic process	7	9	1.004e-02
GO:BP	GO:0015886	heme transport	7	9	1.004e-02
GO:BP	GO:1990481	mRNA pseudouridine synthesis	7	9	1.004e-02
GO:BP	GO:0009101	glycoprotein biosynthetic process	92	300	1.004e-02
GO:BP	GO:0030167	proteoglycan catabolic process	10	16	1.009e-02
GO:BP	GO:0044849	estrous cycle	10	16	1.009e-02
GO:BP	GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	10	16	1.009e-02
GO:BP	GO:0006790	sulfur compound metabolic process	94	308	1.044e-02
GO:BP	GO:0043535	regulation of blood vessel endothelial cell migration	35	93	1.055e-02
GO:BP	GO:0003281	ventricular septum development	29	73	1.067e-02
GO:BP	GO:0009048	dosage compensation by inactivation of X chromosome	13	24	1.086e-02
GO:BP	GO:1901888	regulation of cell junction assembly	82	263	1.088e-02
GO:BP	GO:0007409	axonogenesis	134	463	1.096e-02
GO:BP	GO:0044772	mitotic cell cycle phase transition	125	428	1.108e-02
GO:BP	GO:0097479	synaptic vesicle localization	24	57	1.118e-02
GO:BP	GO:0048511	rhythmic process	93	305	1.134e-02
GO:BP	GO:0043393	regulation of protein binding	41	114	1.134e-02
GO:BP	GO:2000628	regulation of miRNA metabolic process	34	90	1.140e-02
GO:BP	GO:0045444	fat cell differentiation	76	241	1.148e-02
GO:BP	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	23	54	1.171e-02
GO:BP	GO:0044843	cell cycle G1/S phase transition	73	230	1.174e-02
GO:BP	GO:0042594	response to starvation	70	219	1.197e-02
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	14	27	1.198e-02
GO:BP	GO:0030330	DNA damage response, signal transduction by p53 class mediator	22	51	1.212e-02
GO:BP	GO:1990090	cellular response to nerve growth factor stimulus	22	51	1.212e-02
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	61	186	1.212e-02
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	22	51	1.212e-02
GO:BP	GO:1902743	regulation of lamellipodium organization	22	51	1.212e-02
GO:BP	GO:0014910	regulation of smooth muscle cell migration	27	67	1.212e-02
GO:BP	GO:0044091	membrane biogenesis	27	67	1.212e-02
GO:BP	GO:1905037	autophagosome organization	44	125	1.230e-02
GO:BP	GO:1903533	regulation of protein targeting	30	77	1.239e-02
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	168	599	1.249e-02
GO:BP	GO:0042908	xenobiotic transport	21	48	1.257e-02
GO:BP	GO:0051960	regulation of nervous system development	132	457	1.264e-02
GO:BP	GO:1902600	proton transmembrane transport	62	190	1.266e-02
GO:BP	GO:0034620	cellular response to unfolded protein	35	94	1.275e-02
GO:BP	GO:0048524	positive regulation of viral process	26	64	1.281e-02
GO:BP	GO:0045064	T-helper 2 cell differentiation	11	19	1.289e-02
GO:BP	GO:0031623	receptor internalization	47	136	1.306e-02
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	158	560	1.309e-02
GO:BP	GO:0045048	protein insertion into ER membrane	16	33	1.309e-02
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	158	560	1.309e-02
GO:BP	GO:0022604	regulation of cell morphogenesis	77	246	1.311e-02
GO:BP	GO:1990776	response to angiotensin	19	42	1.313e-02
GO:BP	GO:0006901	vesicle coating	18	39	1.319e-02
GO:BP	GO:0014909	smooth muscle cell migration	29	74	1.319e-02
GO:BP	GO:0090049	regulation of cell migration involved in sprouting angiogenesis	18	39	1.319e-02
GO:BP	GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	18	39	1.319e-02
GO:BP	GO:0010591	regulation of lamellipodium assembly	18	39	1.319e-02
GO:BP	GO:0032885	regulation of polysaccharide biosynthetic process	17	36	1.319e-02
GO:BP	GO:1905898	positive regulation of response to endoplasmic reticulum stress	18	39	1.319e-02
GO:BP	GO:0035358	regulation of peroxisome proliferator activated receptor signaling pathway	9	14	1.343e-02
GO:BP	GO:0007018	microtubule-based movement	137	478	1.400e-02
GO:BP	GO:0051098	regulation of binding	68	213	1.400e-02
GO:BP	GO:0030032	lamellipodium assembly	28	71	1.412e-02
GO:BP	GO:0051347	positive regulation of transferase activity	90	296	1.430e-02
GO:BP	GO:0060840	artery development	38	105	1.438e-02
GO:BP	GO:0070646	protein modification by small protein removal	51	151	1.438e-02
GO:BP	GO:0043534	blood vessel endothelial cell migration	42	119	1.445e-02
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	40	112	1.445e-02
GO:BP	GO:0009416	response to light stimulus	97	323	1.460e-02
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	49	144	1.477e-02
GO:BP	GO:0032886	regulation of microtubule-based process	82	266	1.482e-02
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	23	55	1.501e-02
GO:BP	GO:0046902	regulation of mitochondrial membrane permeability	23	55	1.501e-02
GO:BP	GO:0061157	mRNA destabilization	37	102	1.565e-02
GO:BP	GO:1905039	carboxylic acid transmembrane transport	50	148	1.573e-02
GO:BP	GO:0000959	mitochondrial RNA metabolic process	22	52	1.580e-02
GO:BP	GO:0030838	positive regulation of actin filament polymerization	22	52	1.580e-02
GO:BP	GO:0010212	response to ionizing radiation	48	141	1.615e-02
GO:BP	GO:0034605	cellular response to heat	26	65	1.615e-02
GO:BP	GO:0042060	wound healing	125	433	1.659e-02
GO:BP	GO:1904292	regulation of ERAD pathway	13	25	1.665e-02
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	44	127	1.686e-02
GO:BP	GO:0043414	macromolecule methylation	44	127	1.686e-02
GO:BP	GO:0051092	positive regulation of NF-kappaB transcription factor activity	42	120	1.707e-02
GO:BP	GO:0010564	regulation of cell cycle process	197	720	1.707e-02
GO:BP	GO:0050779	RNA destabilization	38	106	1.715e-02
GO:BP	GO:0007020	microtubule nucleation	20	46	1.715e-02
GO:BP	GO:0033673	negative regulation of kinase activity	49	145	1.715e-02
GO:BP	GO:0002831	regulation of response to biotic stimulus	152	540	1.715e-02
GO:BP	GO:0019318	hexose metabolic process	71	226	1.729e-02
GO:BP	GO:0071345	cellular response to cytokine stimulus	230	854	1.741e-02
GO:BP	GO:0070085	glycosylation	76	245	1.756e-02
GO:BP	GO:0047497	mitochondrion transport along microtubule	14	28	1.756e-02
GO:BP	GO:0046112	nucleobase biosynthetic process	10	17	1.756e-02
GO:BP	GO:2001032	regulation of double-strand break repair via nonhomologous end joining	14	28	1.756e-02
GO:BP	GO:0044790	suppression of viral release by host	10	17	1.756e-02
GO:BP	GO:1902175	regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	19	43	1.756e-02
GO:BP	GO:0036508	protein alpha-1,2-demannosylation	10	17	1.756e-02
GO:BP	GO:0036507	protein demannosylation	10	17	1.756e-02
GO:BP	GO:0035672	oligopeptide transmembrane transport	10	17	1.756e-02
GO:BP	GO:0034643	establishment of mitochondrion localization, microtubule-mediated	14	28	1.756e-02
GO:BP	GO:0051881	regulation of mitochondrial membrane potential	28	72	1.756e-02
GO:BP	GO:0010661	positive regulation of muscle cell apoptotic process	14	28	1.756e-02
GO:BP	GO:0001503	ossification	124	430	1.756e-02
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	72	230	1.756e-02
GO:BP	GO:0045628	regulation of T-helper 2 cell differentiation	8	12	1.763e-02
GO:BP	GO:0031293	membrane protein intracellular domain proteolysis	8	12	1.763e-02
GO:BP	GO:0010172	embryonic body morphogenesis	8	12	1.763e-02
GO:BP	GO:0050847	progesterone receptor signaling pathway	8	12	1.763e-02
GO:BP	GO:0060606	tube closure	33	89	1.764e-02
GO:BP	GO:0043543	protein acylation	33	89	1.764e-02
GO:BP	GO:1903900	regulation of viral life cycle	45	131	1.764e-02
GO:BP	GO:1904375	regulation of protein localization to cell periphery	50	149	1.776e-02
GO:BP	GO:0022411	cellular component disassembly	128	446	1.786e-02
GO:BP	GO:0048738	cardiac muscle tissue development	73	234	1.790e-02
GO:BP	GO:1902115	regulation of organelle assembly	73	234	1.790e-02
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	16	34	1.806e-02
GO:BP	GO:0051654	establishment of mitochondrion localization	16	34	1.806e-02
GO:BP	GO:0043516	regulation of DNA damage response, signal transduction by p53 class mediator	16	34	1.806e-02
GO:BP	GO:0032231	regulation of actin filament bundle assembly	37	103	1.819e-02
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	30	79	1.825e-02
GO:BP	GO:0043436	oxoacid metabolic process	243	909	1.914e-02
GO:BP	GO:0003013	circulatory system process	167	602	1.965e-02
GO:BP	GO:0005996	monosaccharide metabolic process	77	250	1.988e-02
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	38	107	2.000e-02
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	47	139	2.002e-02
GO:BP	GO:0008033	tRNA processing	47	139	2.002e-02
GO:BP	GO:1990089	response to nerve growth factor	22	53	2.011e-02
GO:BP	GO:0030097	hemopoiesis	259	976	2.090e-02
GO:BP	GO:0042221	response to chemical	953	3909	2.112e-02
GO:BP	GO:0044788	modulation by host of viral process	21	50	2.127e-02
GO:BP	GO:0002682	regulation of immune system process	405	1581	2.127e-02
GO:BP	GO:0006082	organic acid metabolic process	244	915	2.128e-02
GO:BP	GO:0042692	muscle cell differentiation	117	405	2.128e-02
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	28	73	2.138e-02
GO:BP	GO:0000045	autophagosome assembly	41	118	2.138e-02
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	41	118	2.138e-02
GO:BP	GO:0104004	cellular response to environmental stimulus	100	339	2.160e-02
GO:BP	GO:0071214	cellular response to abiotic stimulus	100	339	2.160e-02
GO:BP	GO:0045785	positive regulation of cell adhesion	138	488	2.169e-02
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	64	202	2.173e-02
GO:BP	GO:0048878	chemical homeostasis	275	1043	2.227e-02
GO:BP	GO:2000736	regulation of stem cell differentiation	30	80	2.243e-02
GO:BP	GO:0030100	regulation of endocytosis	89	297	2.243e-02
GO:BP	GO:0007051	spindle organization	65	206	2.243e-02
GO:BP	GO:0001935	endothelial cell proliferation	52	158	2.255e-02
GO:BP	GO:0032401	establishment of melanosome localization	12	23	2.262e-02
GO:BP	GO:0060052	neurofilament cytoskeleton organization	7	10	2.262e-02
GO:BP	GO:1902965	regulation of protein localization to early endosome	7	10	2.262e-02
GO:BP	GO:0071482	cellular response to light stimulus	42	122	2.262e-02
GO:BP	GO:1904667	negative regulation of ubiquitin protein ligase activity	7	10	2.262e-02
GO:BP	GO:0043124	negative regulation of canonical NF-kappaB signal transduction	24	60	2.262e-02
GO:BP	GO:0180012	co-transcriptional RNA 3’-end processing, cleavage and polyadenylation pathway	7	10	2.262e-02
GO:BP	GO:0006104	succinyl-CoA metabolic process	7	10	2.262e-02
GO:BP	GO:1902966	positive regulation of protein localization to early endosome	7	10	2.262e-02
GO:BP	GO:0000963	mitochondrial RNA processing	12	23	2.262e-02
GO:BP	GO:0048194	Golgi vesicle budding	7	10	2.262e-02
GO:BP	GO:0035443	tripeptide transmembrane transport	7	10	2.262e-02
GO:BP	GO:1902513	regulation of organelle transport along microtubule	7	10	2.262e-02
GO:BP	GO:0030155	regulation of cell adhesion	214	794	2.262e-02
GO:BP	GO:0010907	positive regulation of glucose metabolic process	19	44	2.286e-02
GO:BP	GO:0006650	glycerophospholipid metabolic process	92	309	2.315e-02
GO:BP	GO:0030641	regulation of cellular pH	34	94	2.319e-02
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	38	108	2.321e-02
GO:BP	GO:0003279	cardiac septum development	38	108	2.321e-02
GO:BP	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	9	15	2.373e-02
GO:BP	GO:0061684	chaperone-mediated autophagy	9	15	2.373e-02
GO:BP	GO:0106057	negative regulation of calcineurin-mediated signaling	9	15	2.373e-02
GO:BP	GO:1905666	regulation of protein localization to endosome	9	15	2.373e-02
GO:BP	GO:0106072	negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	9	15	2.373e-02
GO:BP	GO:0061614	miRNA transcription	29	77	2.383e-02
GO:BP	GO:0009267	cellular response to starvation	57	177	2.409e-02
GO:BP	GO:0060765	regulation of androgen receptor signaling pathway	14	29	2.468e-02
GO:BP	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	14	29	2.468e-02
GO:BP	GO:0035872	nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway	14	29	2.468e-02
GO:BP	GO:0006970	response to osmotic stress	31	84	2.468e-02
GO:BP	GO:1904385	cellular response to angiotensin	16	35	2.475e-02
GO:BP	GO:1902369	negative regulation of RNA catabolic process	33	91	2.511e-02
GO:BP	GO:0051492	regulation of stress fiber assembly	33	91	2.511e-02
GO:BP	GO:0006486	protein glycosylation	70	226	2.526e-02
GO:BP	GO:0044782	cilium organization	123	431	2.526e-02
GO:BP	GO:0043413	macromolecule glycosylation	70	226	2.526e-02
GO:BP	GO:0009743	response to carbohydrate	75	245	2.546e-02
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	56	174	2.625e-02
GO:BP	GO:0007265	Ras protein signal transduction	42	123	2.625e-02
GO:BP	GO:1903825	organic acid transmembrane transport	50	152	2.643e-02
GO:BP	GO:1901342	regulation of vasculature development	89	299	2.662e-02
GO:BP	GO:0019752	carboxylic acid metabolic process	236	887	2.675e-02
GO:BP	GO:0099537	trans-synaptic signaling	210	781	2.680e-02
GO:BP	GO:0002064	epithelial cell development	68	219	2.680e-02
GO:BP	GO:0001843	neural tube closure	32	88	2.730e-02
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	34	95	2.755e-02
GO:BP	GO:0016358	dendrite development	74	242	2.771e-02
GO:BP	GO:0043410	positive regulation of MAPK cascade	129	456	2.786e-02
GO:BP	GO:0009605	response to external stimulus	601	2415	2.794e-02
GO:BP	GO:0006695	cholesterol biosynthetic process	24	61	2.799e-02
GO:BP	GO:1902653	secondary alcohol biosynthetic process	24	61	2.799e-02
GO:BP	GO:0071478	cellular response to radiation	58	182	2.806e-02
GO:BP	GO:0061724	lipophagy	6	8	2.806e-02
GO:BP	GO:0051607	defense response to virus	94	319	2.806e-02
GO:BP	GO:2000643	positive regulation of early endosome to late endosome transport	6	8	2.806e-02
GO:BP	GO:0099173	postsynapse organization	75	246	2.806e-02
GO:BP	GO:0034775	glutathione transmembrane transport	6	8	2.806e-02
GO:BP	GO:0070973	protein localization to endoplasmic reticulum exit site	6	8	2.806e-02
GO:BP	GO:0006302	double-strand break repair	94	319	2.806e-02
GO:BP	GO:0034331	cell junction maintenance	20	48	2.808e-02
GO:BP	GO:0032092	positive regulation of protein binding	20	48	2.808e-02
GO:BP	GO:0060443	mammary gland morphogenesis	20	48	2.808e-02
GO:BP	GO:0019896	axonal transport of mitochondrion	10	18	2.814e-02
GO:BP	GO:0003158	endothelium development	46	138	2.815e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	46	138	2.815e-02
GO:BP	GO:0001678	intracellular glucose homeostasis	55	171	2.821e-02
GO:BP	GO:0009611	response to wounding	157	568	2.828e-02
GO:BP	GO:0043489	RNA stabilization	29	78	2.856e-02
GO:BP	GO:0120034	positive regulation of plasma membrane bounded cell projection assembly	39	113	2.884e-02
GO:BP	GO:0043200	response to amino acid	44	131	2.913e-02
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	37	106	2.931e-02
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	19	45	2.942e-02
GO:BP	GO:0030209	dermatan sulfate proteoglycan catabolic process	4	4	2.942e-02
GO:BP	GO:1990180	mitochondrial tRNA 3’-end processing	4	4	2.942e-02
GO:BP	GO:0009791	post-embryonic development	33	92	2.942e-02
GO:BP	GO:1905515	non-motile cilium assembly	26	68	2.942e-02
GO:BP	GO:0032273	positive regulation of protein polymerization	33	92	2.942e-02
GO:BP	GO:0035329	hippo signaling	23	58	2.942e-02
GO:BP	GO:0070373	negative regulation of ERK1 and ERK2 cascade	26	68	2.942e-02
GO:BP	GO:0090148	membrane fission	19	45	2.942e-02
GO:BP	GO:0090261	positive regulation of inclusion body assembly	4	4	2.942e-02
GO:BP	GO:0045860	positive regulation of protein kinase activity	73	239	2.942e-02
GO:BP	GO:0000964	mitochondrial RNA 5’-end processing	4	4	2.942e-02
GO:BP	GO:0035196	miRNA processing	19	45	2.942e-02
GO:BP	GO:0032206	positive regulation of telomere maintenance	28	75	3.078e-02
GO:BP	GO:0003170	heart valve development	28	75	3.078e-02
GO:BP	GO:0032006	regulation of TOR signaling	48	146	3.080e-02
GO:BP	GO:1902904	negative regulation of supramolecular fiber organization	51	157	3.080e-02
GO:BP	GO:0044321	response to leptin	11	21	3.104e-02
GO:BP	GO:0008361	regulation of cell size	58	183	3.106e-02
GO:BP	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	22	55	3.142e-02
GO:BP	GO:0002042	cell migration involved in sprouting angiogenesis	22	55	3.142e-02
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	34	96	3.151e-02
GO:BP	GO:2000354	regulation of ovarian follicle development	5	6	3.151e-02
GO:BP	GO:1901387	positive regulation of voltage-gated calcium channel activity	5	6	3.151e-02
GO:BP	GO:0046627	negative regulation of insulin receptor signaling pathway	17	39	3.151e-02
GO:BP	GO:0048200	Golgi transport vesicle coating	5	6	3.151e-02
GO:BP	GO:0036295	cellular response to increased oxygen levels	8	13	3.151e-02
GO:BP	GO:0031347	regulation of defense response	216	809	3.151e-02
GO:BP	GO:0048205	COPI coating of Golgi vesicle	5	6	3.151e-02
GO:BP	GO:0061795	Golgi lumen acidification	8	13	3.151e-02
GO:BP	GO:0090646	mitochondrial tRNA processing	8	13	3.151e-02
GO:BP	GO:0051276	chromosome organization	158	574	3.151e-02
GO:BP	GO:1902525	regulation of protein monoubiquitination	5	6	3.151e-02
GO:BP	GO:0099547	regulation of translation at synapse, modulating synaptic transmission	5	6	3.151e-02
GO:BP	GO:0010616	negative regulation of cardiac muscle adaptation	5	6	3.151e-02
GO:BP	GO:0032486	Rap protein signal transduction	8	13	3.151e-02
GO:BP	GO:1904386	response to L-phenylalanine derivative	5	6	3.151e-02
GO:BP	GO:0098935	dendritic transport	8	13	3.151e-02
GO:BP	GO:0035964	COPI-coated vesicle budding	5	6	3.151e-02
GO:BP	GO:1903243	negative regulation of cardiac muscle hypertrophy in response to stress	5	6	3.151e-02
GO:BP	GO:0099177	regulation of trans-synaptic signaling	143	514	3.158e-02
GO:BP	GO:0003148	outflow tract septum morphogenesis	12	24	3.238e-02
GO:BP	GO:0051905	establishment of pigment granule localization	12	24	3.238e-02
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	12	24	3.238e-02
GO:BP	GO:0097066	response to thyroid hormone	12	24	3.238e-02
GO:BP	GO:1902745	positive regulation of lamellipodium organization	16	36	3.238e-02
GO:BP	GO:0016485	protein processing	69	225	3.267e-02
GO:BP	GO:0002090	regulation of receptor internalization	27	72	3.267e-02
GO:BP	GO:0071322	cellular response to carbohydrate stimulus	53	165	3.267e-02
GO:BP	GO:0033146	regulation of intracellular estrogen receptor signaling pathway	15	33	3.310e-02
GO:BP	GO:0048199	vesicle targeting, to, from or within Golgi	15	33	3.310e-02
GO:BP	GO:0006929	substrate-dependent cell migration	13	27	3.316e-02
GO:BP	GO:0033119	negative regulation of RNA splicing	13	27	3.316e-02
GO:BP	GO:0048771	tissue remodeling	57	180	3.316e-02
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	75	248	3.316e-02
GO:BP	GO:1901654	response to ketone	70	229	3.322e-02
GO:BP	GO:0034612	response to tumor necrosis factor	70	229	3.322e-02
GO:BP	GO:1902176	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	14	30	3.329e-02
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	29	79	3.344e-02
GO:BP	GO:0008284	positive regulation of cell population proliferation	251	954	3.371e-02
GO:BP	GO:0006006	glucose metabolic process	58	184	3.413e-02
GO:BP	GO:0043467	regulation of generation of precursor metabolites and energy	45	136	3.415e-02
GO:BP	GO:0030218	erythrocyte differentiation	45	136	3.415e-02
GO:BP	GO:0016126	sterol biosynthetic process	26	69	3.527e-02
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	43	129	3.559e-02
GO:BP	GO:0007224	smoothened signaling pathway	49	151	3.592e-02
GO:BP	GO:0007346	regulation of mitotic cell cycle	137	492	3.592e-02
GO:BP	GO:0060612	adipose tissue development	23	59	3.595e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	207	775	3.615e-02
GO:BP	GO:0007268	chemical synaptic transmission	207	775	3.615e-02
GO:BP	GO:0051865	protein autoubiquitination	28	76	3.634e-02
GO:BP	GO:1902893	regulation of miRNA transcription	28	76	3.634e-02
GO:BP	GO:0008285	negative regulation of cell population proliferation	190	706	3.661e-02
GO:BP	GO:0003254	regulation of membrane depolarization	19	46	3.685e-02
GO:BP	GO:0002183	cytoplasmic translational initiation	19	46	3.685e-02
GO:BP	GO:0043039	tRNA aminoacylation	19	46	3.685e-02
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	19	46	3.685e-02
GO:BP	GO:0048525	negative regulation of viral process	30	83	3.685e-02
GO:BP	GO:0033627	cell adhesion mediated by integrin	30	83	3.685e-02
GO:BP	GO:0051453	regulation of intracellular pH	32	90	3.690e-02
GO:BP	GO:0045216	cell-cell junction organization	66	215	3.743e-02
GO:BP	GO:0032984	protein-containing complex disassembly	77	257	3.746e-02
GO:BP	GO:0061450	trophoblast cell migration	9	16	3.794e-02
GO:BP	GO:0099116	tRNA 5’-end processing	9	16	3.794e-02
GO:BP	GO:0038083	peptidyl-tyrosine autophosphorylation	9	16	3.794e-02
GO:BP	GO:1900034	regulation of cellular response to heat	9	16	3.794e-02
GO:BP	GO:0045651	positive regulation of macrophage differentiation	9	16	3.794e-02
GO:BP	GO:0000463	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	9	16	3.794e-02
GO:BP	GO:0030033	microvillus assembly	9	16	3.794e-02
GO:BP	GO:0050804	modulation of chemical synaptic transmission	142	513	3.800e-02
GO:BP	GO:0023061	signal release	139	501	3.800e-02
GO:BP	GO:0045089	positive regulation of innate immune response	107	374	3.804e-02
GO:BP	GO:0006473	protein acetylation	22	56	3.816e-02
GO:BP	GO:0022900	electron transport chain	42	126	3.835e-02
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	18	43	3.866e-02
GO:BP	GO:1903214	regulation of protein targeting to mitochondrion	18	43	3.866e-02
GO:BP	GO:0110020	regulation of actomyosin structure organization	35	101	3.922e-02
GO:BP	GO:0090398	cellular senescence	35	101	3.922e-02
GO:BP	GO:1902414	protein localization to cell junction	40	119	3.965e-02
GO:BP	GO:0039531	regulation of cytoplasmic pattern recognition receptor signaling pathway	40	119	3.965e-02
GO:BP	GO:0048259	regulation of receptor-mediated endocytosis	40	119	3.965e-02
GO:BP	GO:0014020	primary neural tube formation	33	94	3.970e-02
GO:BP	GO:0033674	positive regulation of kinase activity	76	254	4.030e-02
GO:BP	GO:1902686	mitochondrial outer membrane permeabilization involved in programmed cell death	17	40	4.050e-02
GO:BP	GO:0051893	regulation of focal adhesion assembly	24	63	4.050e-02
GO:BP	GO:0014911	positive regulation of smooth muscle cell migration	17	40	4.050e-02
GO:BP	GO:1900077	negative regulation of cellular response to insulin stimulus	17	40	4.050e-02
GO:BP	GO:0002757	immune response-activating signaling pathway	137	494	4.050e-02
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	24	63	4.050e-02
GO:BP	GO:0090109	regulation of cell-substrate junction assembly	24	63	4.050e-02
GO:BP	GO:0051403	stress-activated MAPK cascade	21	53	4.071e-02
GO:BP	GO:0071824	protein-DNA complex organization	78	262	4.131e-02
GO:BP	GO:0045765	regulation of angiogenesis	86	293	4.150e-02
GO:BP	GO:0090085	regulation of protein deubiquitination	7	11	4.168e-02
GO:BP	GO:0048490	anterograde synaptic vesicle transport	10	19	4.168e-02
GO:BP	GO:0006307	DNA alkylation repair	7	11	4.168e-02
GO:BP	GO:0070213	protein auto-ADP-ribosylation	7	11	4.168e-02
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	26	70	4.168e-02
GO:BP	GO:0006607	NLS-bearing protein import into nucleus	10	19	4.168e-02
GO:BP	GO:0002158	osteoclast proliferation	7	11	4.168e-02
GO:BP	GO:0006144	purine nucleobase metabolic process	10	19	4.168e-02
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	10	19	4.168e-02
GO:BP	GO:1905383	protein localization to presynapse	7	11	4.168e-02
GO:BP	GO:0008203	cholesterol metabolic process	47	145	4.168e-02
GO:BP	GO:0034284	response to monosaccharide	67	220	4.168e-02
GO:BP	GO:0001101	response to acid chemical	47	145	4.168e-02
GO:BP	GO:0051580	regulation of neurotransmitter uptake	10	19	4.168e-02
GO:BP	GO:0099517	synaptic vesicle transport along microtubule	10	19	4.168e-02
GO:BP	GO:0016479	negative regulation of transcription by RNA polymerase I	7	11	4.168e-02
GO:BP	GO:0099514	synaptic vesicle cytoskeletal transport	10	19	4.168e-02
GO:BP	GO:0006857	oligopeptide transport	10	19	4.168e-02
GO:BP	GO:0099536	synaptic signaling	214	807	4.197e-02
GO:BP	GO:0046785	microtubule polymerization	34	98	4.202e-02
GO:BP	GO:1901987	regulation of cell cycle phase transition	120	427	4.202e-02
GO:BP	GO:0009887	animal organ morphogenesis	271	1042	4.237e-02
GO:BP	GO:0002683	negative regulation of immune system process	142	515	4.242e-02
GO:BP	GO:0007004	telomere maintenance via telomerase	23	60	4.321e-02
GO:BP	GO:0009112	nucleobase metabolic process	15	34	4.335e-02
GO:BP	GO:0140058	neuron projection arborization	15	34	4.335e-02
GO:BP	GO:0060538	skeletal muscle organ development	60	194	4.378e-02
GO:BP	GO:0060429	epithelium development	318	1238	4.384e-02
GO:BP	GO:0048025	negative regulation of mRNA splicing, via spliceosome	11	22	4.394e-02
GO:BP	GO:0009746	response to hexose	65	213	4.394e-02
GO:BP	GO:0060008	Sertoli cell differentiation	11	22	4.394e-02
GO:BP	GO:0006907	pinocytosis	11	22	4.394e-02
GO:BP	GO:0032402	melanosome transport	11	22	4.394e-02
GO:BP	GO:0019082	viral protein processing	14	31	4.442e-02
GO:BP	GO:0060147	regulation of post-transcriptional gene silencing	14	31	4.442e-02
GO:BP	GO:0000470	maturation of LSU-rRNA	12	25	4.464e-02
GO:BP	GO:0061339	establishment or maintenance of monopolar cell polarity	12	25	4.464e-02
GO:BP	GO:0051147	regulation of muscle cell differentiation	46	142	4.464e-02
GO:BP	GO:0036296	response to increased oxygen levels	13	28	4.464e-02
GO:BP	GO:0006665	sphingolipid metabolic process	53	168	4.464e-02
GO:BP	GO:0045624	positive regulation of T-helper cell differentiation	12	25	4.464e-02
GO:BP	GO:0060155	platelet dense granule organization	12	25	4.464e-02
GO:BP	GO:0099558	maintenance of synapse structure	13	28	4.464e-02
GO:BP	GO:0005979	regulation of glycogen biosynthetic process	13	28	4.464e-02
GO:BP	GO:0032400	melanosome localization	12	25	4.464e-02
GO:BP	GO:0010962	regulation of glucan biosynthetic process	13	28	4.464e-02
GO:BP	GO:0033598	mammary gland epithelial cell proliferation	13	28	4.464e-02
GO:BP	GO:0035020	regulation of Rac protein signal transduction	12	25	4.464e-02
GO:BP	GO:0035994	response to muscle stretch	12	25	4.464e-02
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	13	28	4.464e-02
GO:BP	GO:0071396	cellular response to lipid	166	613	4.516e-02
GO:BP	GO:0010634	positive regulation of epithelial cell migration	19	47	4.523e-02
GO:BP	GO:0036465	synaptic vesicle recycling	33	95	4.523e-02
GO:BP	GO:0043038	amino acid activation	19	47	4.523e-02
GO:BP	GO:0042982	amyloid precursor protein metabolic process	27	74	4.549e-02
GO:BP	GO:0045824	negative regulation of innate immune response	31	88	4.574e-02
GO:BP	GO:0001510	RNA methylation	29	81	4.575e-02
GO:BP	GO:0060395	SMAD protein signal transduction	29	81	4.575e-02
GO:BP	GO:0031098	stress-activated protein kinase signaling cascade	22	57	4.575e-02
GO:BP	GO:0009755	hormone-mediated signaling pathway	68	225	4.575e-02
GO:BP	GO:0051851	host-mediated perturbation of symbiont process	36	106	4.720e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	55	176	4.720e-02
GO:BP	GO:0060759	regulation of response to cytokine stimulus	55	176	4.720e-02
GO:BP	GO:0050673	epithelial cell proliferation	123	441	4.783e-02
GO:BP	GO:0032881	regulation of polysaccharide metabolic process	18	44	4.814e-02
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	24	64	4.814e-02
GO:BP	GO:0016079	synaptic vesicle exocytosis	34	99	4.837e-02
GO:BP	GO:0007519	skeletal muscle tissue development	56	180	4.847e-02
GO:BP	GO:0001959	regulation of cytokine-mediated signaling pathway	52	165	4.851e-02
GO:BP	GO:0051899	membrane depolarization	32	92	4.929e-02
GO:BP	GO:0071230	cellular response to amino acid stimulus	32	92	4.929e-02
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	26	71	4.932e-02
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	26	71	4.932e-02
GO:BP	GO:0006360	transcription by RNA polymerase I	26	71	4.932e-02
GO:BP	GO:0048863	stem cell differentiation	73	245	4.935e-02
GO:BP	GO:0003205	cardiac chamber development	53	169	4.985e-02
GO:BP	GO:1904018	positive regulation of vasculature development	53	169	4.985e-02
KEGG	KEGG:05132	Salmonella infection	111	249	1.529e-06
KEGG	KEGG:04144	Endocytosis	107	248	1.215e-05
KEGG	KEGG:04510	Focal adhesion	89	202	3.360e-05
KEGG	KEGG:05012	Parkinson disease	109	265	8.427e-05
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	65	140	8.950e-05
KEGG	KEGG:04142	Lysosome	61	131	1.195e-04
KEGG	KEGG:03010	Ribosome	69	153	1.195e-04
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	172	474	5.852e-04
KEGG	KEGG:05171	Coronavirus disease - COVID-19	92	231	1.201e-03
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	70	168	1.782e-03
KEGG	KEGG:04012	ErbB signaling pathway	40	84	2.170e-03
KEGG	KEGG:05010	Alzheimer disease	138	382	3.556e-03
KEGG	KEGG:03083	Polycomb repressive complex	39	84	4.141e-03
KEGG	KEGG:05016	Huntington disease	113	305	4.141e-03
KEGG	KEGG:05205	Proteoglycans in cancer	80	205	5.120e-03
KEGG	KEGG:04148	Efferocytosis	63	156	7.401e-03
KEGG	KEGG:04722	Neurotrophin signaling pathway	50	118	7.421e-03
KEGG	KEGG:05211	Renal cell carcinoma	32	68	9.001e-03
KEGG	KEGG:05168	Herpes simplex virus 1 infection	172	506	1.108e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	128	363	1.108e-02
KEGG	KEGG:04933	AGE-RAGE signaling pathway in diabetic complications	43	100	1.108e-02
KEGG	KEGG:05020	Prion disease	98	271	1.669e-02
KEGG	KEGG:05415	Diabetic cardiomyopathy	76	202	1.669e-02
KEGG	KEGG:04962	Vasopressin-regulated water reabsorption	22	44	1.896e-02
KEGG	KEGG:04910	Insulin signaling pathway	54	137	2.360e-02
KEGG	KEGG:05220	Chronic myeloid leukemia	33	76	2.861e-02
KEGG	KEGG:04015	Rap1 signaling pathway	77	210	3.027e-02
KEGG	KEGG:04919	Thyroid hormone signaling pathway	48	121	3.181e-02
KEGG	KEGG:04810	Regulation of actin cytoskeleton	82	227	3.240e-02
KEGG	KEGG:04150	mTOR signaling pathway	59	155	3.240e-02
KEGG	KEGG:04310	Wnt signaling pathway	65	174	3.345e-02
KEGG	KEGG:04668	TNF signaling pathway	45	113	3.418e-02
KEGG	KEGG:04714	Thermogenesis	83	232	3.776e-02
KEGG	KEGG:05110	Vibrio cholerae infection	23	50	4.167e-02
KEGG	KEGG:05212	Pancreatic cancer	32	76	4.401e-02

# write.csv(table_motif1_GOKEGG_genes, "data/new/table_motif1_GOKEGG_genes.csv")

#GO:BP
table_motif1_genes_GOBP <- table_motif1_GOKEGG_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif1_genes_GOBP, "data/table_motif1_genes_GOBP.RDS")

table_motif1_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 1 Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_motif1_genes_KEGG <- table_motif1_GOKEGG_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif1_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 1 DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####Motif 2 Genes#####
# motif2_genes_matrix <- as.matrix(final_genes_2) 
# colnames(motif2_genes_matrix) <- c("entrezgene_ID")

# saveRDS(motif2_genes_matrix, "data/new/motif2_genes_matrix.RDS")
motif2_genes_matrix <- readRDS("data/new/motif2_genes_matrix.RDS")
length(motif2_genes_matrix)

[1] 6218

#6218 genes in this set for motif 2

motif2_mat_GOKEGG <- gost(query = motif2_genes_matrix,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif2_GOKEGG_genes <- gostplot(motif2_mat_GOKEGG, capped = FALSE, interactive = TRUE)
motif2_GOKEGG_genes

table_motif2_GOKEGG_genes <- motif2_mat_GOKEGG$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif2_GOKEGG_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0080090	regulation of primary metabolic process	1774	5390	3.227e-49
GO:BP	GO:0019538	protein metabolic process	1570	4721	7.436e-45
GO:BP	GO:0048518	positive regulation of biological process	1969	6264	1.103e-40
GO:BP	GO:0048522	positive regulation of cellular process	1874	5920	3.472e-40
GO:BP	GO:0050789	regulation of biological process	3502	12336	4.738e-40
GO:BP	GO:0065007	biological regulation	3594	12743	5.343e-39
GO:BP	GO:0050794	regulation of cellular process	3398	11946	2.649e-38
GO:BP	GO:0006996	organelle organization	1221	3594	1.195e-37
GO:BP	GO:0051128	regulation of cellular component organization	883	2433	3.931e-37
GO:BP	GO:0043412	macromolecule modification	1047	3030	1.239e-34
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	1314	3990	1.034e-33
GO:BP	GO:0007275	multicellular organism development	1515	4727	2.679e-33
GO:BP	GO:0048856	anatomical structure development	1846	5997	3.191e-31
GO:BP	GO:0051252	regulation of RNA metabolic process	1217	3687	3.740e-31
GO:BP	GO:0006351	DNA-templated transcription	1177	3549	6.798e-31
GO:BP	GO:0032502	developmental process	1975	6553	3.668e-28
GO:BP	GO:0036211	protein modification process	964	2846	6.886e-28
GO:BP	GO:0048731	system development	1302	4053	6.886e-28
GO:BP	GO:0006355	regulation of DNA-templated transcription	1119	3409	4.575e-27
GO:BP	GO:2001141	regulation of RNA biosynthetic process	1124	3428	5.033e-27
GO:BP	GO:0009056	catabolic process	895	2639	8.883e-26
GO:BP	GO:0009893	positive regulation of metabolic process	1161	3597	4.474e-25
GO:BP	GO:0006796	phosphate-containing compound metabolic process	825	2407	4.595e-25
GO:BP	GO:0006793	phosphorus metabolic process	825	2410	6.885e-25
GO:BP	GO:0019222	regulation of metabolic process	2071	7035	1.584e-23
GO:BP	GO:0048583	regulation of response to stimulus	1259	3993	4.220e-23
GO:BP	GO:0010646	regulation of cell communication	1117	3486	1.193e-22
GO:BP	GO:0023051	regulation of signaling	1110	3478	8.795e-22
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	1057	3288	1.007e-21
GO:BP	GO:0009966	regulation of signal transduction	985	3034	1.697e-21
GO:BP	GO:0033554	cellular response to stress	641	1830	1.914e-21
GO:BP	GO:0035556	intracellular signal transduction	962	2965	8.139e-21
GO:BP	GO:0030030	cell projection organization	579	1631	1.174e-20
GO:BP	GO:0051179	localization	1663	5555	1.281e-20
GO:BP	GO:0051716	cellular response to stimulus	2137	7376	2.177e-20
GO:BP	GO:0006366	transcription by RNA polymerase II	887	2711	3.869e-20
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	691	2036	2.503e-19
GO:BP	GO:0006810	transport	1347	4407	3.580e-19
GO:BP	GO:0009653	anatomical structure morphogenesis	882	2713	4.127e-19
GO:BP	GO:0007399	nervous system development	851	2604	4.771e-19
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	559	1588	5.185e-19
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	843	2578	6.143e-19
GO:BP	GO:0060255	regulation of macromolecule metabolic process	1895	6492	1.101e-18
GO:BP	GO:0051641	cellular localization	1141	3661	1.275e-18
GO:BP	GO:0051254	positive regulation of RNA metabolic process	626	1835	6.459e-18
GO:BP	GO:0033043	regulation of organelle organization	423	1148	6.646e-18
GO:BP	GO:0044087	regulation of cellular component biogenesis	381	1011	7.423e-18
GO:BP	GO:0048523	negative regulation of cellular process	1660	5629	1.786e-17
GO:BP	GO:0019637	organophosphate metabolic process	399	1077	2.758e-17
GO:BP	GO:0007507	heart development	250	605	6.291e-17
GO:BP	GO:0022008	neurogenesis	600	1771	2.225e-16
GO:BP	GO:0044281	small molecule metabolic process	601	1776	2.646e-16
GO:BP	GO:0048519	negative regulation of biological process	1705	5834	2.646e-16
GO:BP	GO:0044238	primary metabolic process	3350	12342	2.817e-16
GO:BP	GO:0048869	cellular developmental process	1335	4438	3.013e-16
GO:BP	GO:0030154	cell differentiation	1334	4437	3.781e-16
GO:BP	GO:0072359	circulatory system development	412	1145	1.953e-15
GO:BP	GO:0048699	generation of neurons	526	1536	3.587e-15
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	573	1699	3.778e-15
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	572	1697	4.537e-15
GO:BP	GO:0009894	regulation of catabolic process	378	1040	7.529e-15
GO:BP	GO:0033036	macromolecule localization	997	3228	1.274e-14
GO:BP	GO:0051246	regulation of protein metabolic process	614	1855	1.902e-14
GO:BP	GO:0040007	growth	342	929	3.007e-14
GO:BP	GO:0070727	cellular macromolecule localization	872	2782	3.257e-14
GO:BP	GO:0051649	establishment of localization in cell	656	2010	4.283e-14
GO:BP	GO:0051234	establishment of localization	1449	4928	4.417e-14
GO:BP	GO:0046907	intracellular transport	475	1381	5.601e-14
GO:BP	GO:0051239	regulation of multicellular organismal process	918	2956	5.997e-14
GO:BP	GO:0050896	response to stimulus	2498	8999	6.284e-14
GO:BP	GO:0009057	macromolecule catabolic process	485	1417	6.809e-14
GO:BP	GO:0008104	protein localization	866	2770	7.996e-14
GO:BP	GO:0009891	positive regulation of biosynthetic process	845	2696	9.883e-14
GO:BP	GO:1901135	carbohydrate derivative metabolic process	356	983	1.004e-13
GO:BP	GO:0050793	regulation of developmental process	778	2457	1.340e-13
GO:BP	GO:0032879	regulation of localization	658	2029	1.524e-13
GO:BP	GO:0030182	neuron differentiation	493	1451	1.549e-13
GO:BP	GO:0032501	multicellular organismal process	2067	7322	1.601e-13
GO:BP	GO:0007010	cytoskeleton organization	513	1529	4.898e-13
GO:BP	GO:0012501	programmed cell death	642	1987	8.067e-13
GO:BP	GO:0008219	cell death	643	1991	8.384e-13
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	810	2593	9.995e-13
GO:BP	GO:0009889	regulation of biosynthetic process	1668	5809	1.185e-12
GO:BP	GO:0048468	cell development	887	2876	1.242e-12
GO:BP	GO:0061061	muscle structure development	263	693	1.422e-12
GO:BP	GO:0065008	regulation of biological quality	905	2947	1.961e-12
GO:BP	GO:0031175	neuron projection development	362	1023	2.285e-12
GO:BP	GO:0140053	mitochondrial gene expression	88	168	2.661e-12
GO:BP	GO:0006915	apoptotic process	620	1923	3.674e-12
GO:BP	GO:0016049	cell growth	196	485	3.812e-12
GO:BP	GO:0007154	cell communication	1851	6540	6.232e-12
GO:BP	GO:0016192	vesicle-mediated transport	525	1592	6.232e-12
GO:BP	GO:0051130	positive regulation of cellular component organization	384	1105	6.795e-12
GO:BP	GO:0008033	tRNA processing	76	139	7.709e-12
GO:BP	GO:0030029	actin filament-based process	300	825	9.511e-12
GO:BP	GO:0007166	cell surface receptor signaling pathway	865	2819	9.879e-12
GO:BP	GO:0022411	cellular component disassembly	182	446	1.035e-11
GO:BP	GO:0048666	neuron development	404	1177	1.107e-11
GO:BP	GO:0023052	signaling	1842	6515	1.110e-11
GO:BP	GO:0006399	tRNA metabolic process	102	210	1.236e-11
GO:BP	GO:0048513	animal organ development	935	3085	2.029e-11
GO:BP	GO:0070925	organelle assembly	363	1046	3.930e-11
GO:BP	GO:0061024	membrane organization	296	821	4.274e-11
GO:BP	GO:0051129	negative regulation of cellular component organization	259	701	6.300e-11
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1609	5644	6.478e-11
GO:BP	GO:0040008	regulation of growth	229	604	7.040e-11
GO:BP	GO:1902531	regulation of intracellular signal transduction	620	1953	8.137e-11
GO:BP	GO:0009790	embryo development	387	1135	9.965e-11
GO:BP	GO:0071840	cellular component organization or biogenesis	2313	8393	9.965e-11
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	500	1529	1.054e-10
GO:BP	GO:0032984	protein-containing complex disassembly	116	257	1.348e-10
GO:BP	GO:0015031	protein transport	475	1444	1.464e-10
GO:BP	GO:0042692	muscle cell differentiation	165	405	1.507e-10
GO:BP	GO:0006259	DNA metabolic process	348	1005	1.519e-10
GO:BP	GO:0060537	muscle tissue development	173	430	1.519e-10
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	283	786	1.519e-10
GO:BP	GO:0032543	mitochondrial translation	70	130	1.605e-10
GO:BP	GO:0042254	ribosome biogenesis	138	323	1.629e-10
GO:BP	GO:0141124	intracellular signaling cassette	606	1912	1.923e-10
GO:BP	GO:0060047	heart contraction	111	244	2.034e-10
GO:BP	GO:0009896	positive regulation of catabolic process	209	546	2.229e-10
GO:BP	GO:0080135	regulation of cellular response to stress	200	519	3.229e-10
GO:BP	GO:0016072	rRNA metabolic process	118	266	3.253e-10
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	238	643	3.805e-10
GO:BP	GO:0009888	tissue development	637	2032	4.351e-10
GO:BP	GO:0030163	protein catabolic process	353	1030	4.368e-10
GO:BP	GO:0006281	DNA repair	231	621	4.379e-10
GO:BP	GO:0006950	response to stress	1155	3948	4.691e-10
GO:BP	GO:0006974	DNA damage response	317	908	4.691e-10
GO:BP	GO:0007165	signal transduction	1693	6002	4.834e-10
GO:BP	GO:0031344	regulation of cell projection organization	242	658	5.056e-10
GO:BP	GO:0003015	heart process	113	253	5.079e-10
GO:BP	GO:0023057	negative regulation of signaling	469	1435	5.236e-10
GO:BP	GO:0010648	negative regulation of cell communication	469	1436	5.847e-10
GO:BP	GO:0044057	regulation of system process	209	553	8.034e-10
GO:BP	GO:0043067	regulation of programmed cell death	488	1506	8.038e-10
GO:BP	GO:0048585	negative regulation of response to stimulus	537	1680	8.038e-10
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	223	599	8.657e-10
GO:BP	GO:0051049	regulation of transport	516	1607	9.573e-10
GO:BP	GO:0010468	regulation of gene expression	1568	5536	1.205e-09
GO:BP	GO:0019941	modification-dependent protein catabolic process	234	638	1.446e-09
GO:BP	GO:0030036	actin cytoskeleton organization	261	729	1.852e-09
GO:BP	GO:0005975	carbohydrate metabolic process	210	561	1.890e-09
GO:BP	GO:0014706	striated muscle tissue development	162	408	2.139e-09
GO:BP	GO:0006936	muscle contraction	143	349	2.210e-09
GO:BP	GO:0009968	negative regulation of signal transduction	434	1326	2.527e-09
GO:BP	GO:0000902	cell morphogenesis	339	996	2.634e-09
GO:BP	GO:0065009	regulation of molecular function	482	1496	2.639e-09
GO:BP	GO:0001558	regulation of cell growth	161	406	2.674e-09
GO:BP	GO:0006400	tRNA modification	54	95	2.707e-09
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	234	642	2.725e-09
GO:BP	GO:0071705	nitrogen compound transport	601	1923	2.827e-09
GO:BP	GO:0003012	muscle system process	171	438	2.850e-09
GO:BP	GO:0097435	supramolecular fiber organization	299	861	3.187e-09
GO:BP	GO:0006937	regulation of muscle contraction	80	165	3.912e-09
GO:BP	GO:0006091	generation of precursor metabolites and energy	183	478	3.983e-09
GO:BP	GO:0042981	regulation of apoptotic process	471	1462	4.339e-09
GO:BP	GO:0090407	organophosphate biosynthetic process	226	619	4.713e-09
GO:BP	GO:0006753	nucleoside phosphate metabolic process	234	646	5.146e-09
GO:BP	GO:0051253	negative regulation of RNA metabolic process	453	1400	5.178e-09
GO:BP	GO:0042592	homeostatic process	547	1736	5.616e-09
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	200	535	5.722e-09
GO:BP	GO:0072524	pyridine-containing compound metabolic process	81	169	5.859e-09
GO:BP	GO:0048858	cell projection morphogenesis	244	681	6.688e-09
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	228	628	6.825e-09
GO:BP	GO:0009987	cellular process	5127	20247	6.964e-09
GO:BP	GO:0018193	peptidyl-amino acid modification	245	686	8.613e-09
GO:BP	GO:0048589	developmental growth	238	663	9.014e-09
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	241	673	9.014e-09
GO:BP	GO:0048738	cardiac muscle tissue development	103	234	9.357e-09
GO:BP	GO:0019362	pyridine nucleotide metabolic process	78	162	9.357e-09
GO:BP	GO:0046496	nicotinamide nucleotide metabolic process	78	162	9.357e-09
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	410	1256	1.156e-08
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	241	676	1.425e-08
GO:BP	GO:0006412	translation	256	727	1.574e-08
GO:BP	GO:0048812	neuron projection morphogenesis	236	660	1.579e-08
GO:BP	GO:0061919	process utilizing autophagic mechanism	217	597	1.595e-08
GO:BP	GO:0006914	autophagy	217	597	1.595e-08
GO:BP	GO:0008016	regulation of heart contraction	92	204	1.807e-08
GO:BP	GO:0006364	rRNA processing	99	225	2.076e-08
GO:BP	GO:0009719	response to endogenous stimulus	474	1489	2.193e-08
GO:BP	GO:0048584	positive regulation of response to stimulus	706	2331	2.360e-08
GO:BP	GO:0006163	purine nucleotide metabolic process	165	430	2.450e-08
GO:BP	GO:1902903	regulation of supramolecular fiber organization	150	383	2.874e-08
GO:BP	GO:0034330	cell junction organization	286	834	3.199e-08
GO:BP	GO:0006941	striated muscle contraction	86	189	3.793e-08
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	325	970	4.020e-08
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	413	1280	4.794e-08
GO:BP	GO:0099173	postsynapse organization	105	246	4.794e-08
GO:BP	GO:0090257	regulation of muscle system process	100	231	4.794e-08
GO:BP	GO:0043687	post-translational protein modification	341	1027	4.794e-08
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	214	594	4.794e-08
GO:BP	GO:0051146	striated muscle cell differentiation	123	301	4.847e-08
GO:BP	GO:0051726	regulation of cell cycle	358	1087	5.052e-08
GO:BP	GO:0008610	lipid biosynthetic process	254	729	5.325e-08
GO:BP	GO:0060048	cardiac muscle contraction	69	142	5.667e-08
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	417	1296	5.719e-08
GO:BP	GO:0016055	Wnt signaling pathway	172	458	6.609e-08
GO:BP	GO:0072521	purine-containing compound metabolic process	204	563	6.633e-08
GO:BP	GO:0050808	synapse organization	204	563	6.633e-08
GO:BP	GO:0051493	regulation of cytoskeleton organization	190	517	6.801e-08
GO:BP	GO:0006629	lipid metabolic process	443	1391	7.351e-08
GO:BP	GO:0016310	phosphorylation	423	1320	7.451e-08
GO:BP	GO:0006942	regulation of striated muscle contraction	52	97	8.041e-08
GO:BP	GO:0006302	double-strand break repair	128	319	8.240e-08
GO:BP	GO:0006644	phospholipid metabolic process	151	392	8.785e-08
GO:BP	GO:0055001	muscle cell development	88	198	9.288e-08
GO:BP	GO:0043414	macromolecule methylation	63	127	9.917e-08
GO:BP	GO:0010498	proteasomal protein catabolic process	197	543	1.089e-07
GO:BP	GO:0006508	proteolysis	468	1486	1.254e-07
GO:BP	GO:0071495	cellular response to endogenous stimulus	394	1223	1.354e-07
GO:BP	GO:0080134	regulation of response to stress	440	1387	1.407e-07
GO:BP	GO:0051604	protein maturation	195	539	1.668e-07
GO:BP	GO:0045184	establishment of protein localization	591	1937	2.055e-07
GO:BP	GO:0009967	positive regulation of signal transduction	492	1578	2.129e-07
GO:BP	GO:0009117	nucleotide metabolic process	180	493	3.037e-07
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	385	1199	3.115e-07
GO:BP	GO:0043009	chordate embryonic development	233	671	3.333e-07
GO:BP	GO:0060341	regulation of cellular localization	332	1013	3.398e-07
GO:BP	GO:0006325	chromatin organization	295	884	3.398e-07
GO:BP	GO:0032446	protein modification by small protein conjugation	286	853	3.460e-07
GO:BP	GO:0048729	tissue morphogenesis	216	614	3.497e-07
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	321	975	3.548e-07
GO:BP	GO:0051247	positive regulation of protein metabolic process	339	1039	3.937e-07
GO:BP	GO:0055002	striated muscle cell development	77	171	4.309e-07
GO:BP	GO:0009451	RNA modification	78	174	4.402e-07
GO:BP	GO:0030031	cell projection assembly	215	613	4.913e-07
GO:BP	GO:0016043	cellular component organization	2216	8184	4.969e-07
GO:BP	GO:0044283	small molecule biosynthetic process	209	593	5.023e-07
GO:BP	GO:0010647	positive regulation of cell communication	549	1795	5.073e-07
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	238	692	5.599e-07
GO:BP	GO:0006886	intracellular protein transport	236	686	6.260e-07
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	120	304	7.139e-07
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	120	304	7.139e-07
GO:BP	GO:0019752	carboxylic acid metabolic process	294	887	7.139e-07
GO:BP	GO:0031400	negative regulation of protein modification process	134	349	7.927e-07
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	210	600	8.444e-07
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	154	414	8.444e-07
GO:BP	GO:0007049	cell cycle	511	1663	8.507e-07
GO:BP	GO:0051052	regulation of DNA metabolic process	180	500	9.001e-07
GO:BP	GO:0009166	nucleotide catabolic process	73	162	9.353e-07
GO:BP	GO:0023056	positive regulation of signaling	547	1796	9.843e-07
GO:BP	GO:0006650	glycerophospholipid metabolic process	121	309	1.030e-06
GO:BP	GO:0043244	regulation of protein-containing complex disassembly	61	128	1.055e-06
GO:BP	GO:0001701	in utero embryonic development	153	413	1.244e-06
GO:BP	GO:0003007	heart morphogenesis	107	266	1.268e-06
GO:BP	GO:0010975	regulation of neuron projection development	163	446	1.278e-06
GO:BP	GO:0051094	positive regulation of developmental process	421	1343	1.337e-06
GO:BP	GO:0008654	phospholipid biosynthetic process	104	257	1.354e-06
GO:BP	GO:0060485	mesenchyme development	124	320	1.372e-06
GO:BP	GO:0009628	response to abiotic stimulus	365	1144	1.488e-06
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	276	831	1.507e-06
GO:BP	GO:0006082	organic acid metabolic process	300	915	1.550e-06
GO:BP	GO:0055117	regulation of cardiac muscle contraction	41	75	1.660e-06
GO:BP	GO:1901292	nucleoside phosphate catabolic process	80	185	1.789e-06
GO:BP	GO:0061564	axon development	187	528	1.789e-06
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	180	505	1.904e-06
GO:BP	GO:0072526	pyridine-containing compound catabolic process	51	102	1.965e-06
GO:BP	GO:0070887	cellular response to chemical stimulus	652	2192	2.008e-06
GO:BP	GO:0035239	tube morphogenesis	289	879	2.024e-06
GO:BP	GO:0006282	regulation of DNA repair	93	225	2.085e-06
GO:BP	GO:1903522	regulation of blood circulation	103	256	2.120e-06
GO:BP	GO:0009261	ribonucleotide catabolic process	63	136	2.224e-06
GO:BP	GO:0007409	axonogenesis	167	463	2.283e-06
GO:BP	GO:0001510	RNA methylation	43	81	2.345e-06
GO:BP	GO:0043436	oxoacid metabolic process	297	909	2.500e-06
GO:BP	GO:0030239	myofibril assembly	41	76	2.603e-06
GO:BP	GO:0032880	regulation of protein localization	296	907	2.954e-06
GO:BP	GO:0006468	protein phosphorylation	386	1227	3.144e-06
GO:BP	GO:0016567	protein ubiquitination	256	768	3.144e-06
GO:BP	GO:0010638	positive regulation of organelle organization	175	492	3.269e-06
GO:BP	GO:0019751	polyol metabolic process	53	109	3.369e-06
GO:BP	GO:1903311	regulation of mRNA metabolic process	120	312	3.381e-06
GO:BP	GO:0008152	metabolic process	3683	14136	3.437e-06
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	225	662	3.488e-06
GO:BP	GO:0048878	chemical homeostasis	334	1043	3.542e-06
GO:BP	GO:0072523	purine-containing compound catabolic process	69	155	3.547e-06
GO:BP	GO:0051240	positive regulation of multicellular organismal process	507	1667	3.639e-06
GO:BP	GO:0045595	regulation of cell differentiation	482	1576	3.679e-06
GO:BP	GO:0006195	purine nucleotide catabolic process	63	138	4.086e-06
GO:BP	GO:0010639	negative regulation of organelle organization	132	352	4.284e-06
GO:BP	GO:0045017	glycerolipid biosynthetic process	100	250	4.307e-06
GO:BP	GO:0031399	regulation of protein modification process	335	1049	4.479e-06
GO:BP	GO:0010882	regulation of cardiac muscle contraction by calcium ion signaling	20	27	4.767e-06
GO:BP	GO:0046488	phosphatidylinositol metabolic process	71	162	4.814e-06
GO:BP	GO:0019364	pyridine nucleotide catabolic process	49	99	4.866e-06
GO:BP	GO:0070848	response to growth factor	241	721	5.546e-06
GO:BP	GO:0031346	positive regulation of cell projection organization	133	357	5.789e-06
GO:BP	GO:0016358	dendrite development	97	242	5.789e-06
GO:BP	GO:0003013	circulatory system process	206	602	6.588e-06
GO:BP	GO:0048762	mesenchymal cell differentiation	100	252	6.588e-06
GO:BP	GO:0046434	organophosphate catabolic process	98	246	6.986e-06
GO:BP	GO:0060560	developmental growth involved in morphogenesis	96	240	7.388e-06
GO:BP	GO:0046486	glycerolipid metabolic process	145	398	7.684e-06
GO:BP	GO:0035295	tube development	348	1101	7.716e-06
GO:BP	GO:2000026	regulation of multicellular organismal development	436	1418	7.740e-06
GO:BP	GO:0062197	cellular response to chemical stress	120	317	8.474e-06
GO:BP	GO:0032790	ribosome disassembly	26	41	8.512e-06
GO:BP	GO:0051051	negative regulation of transport	149	412	8.637e-06
GO:BP	GO:0006457	protein folding	89	219	8.677e-06
GO:BP	GO:0009154	purine ribonucleotide catabolic process	59	129	8.839e-06
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	213	629	9.551e-06
GO:BP	GO:1901136	carbohydrate derivative catabolic process	101	257	9.551e-06
GO:BP	GO:0048588	developmental cell growth	91	226	1.029e-05
GO:BP	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	21	30	1.029e-05
GO:BP	GO:0019318	hexose metabolic process	91	226	1.029e-05
GO:BP	GO:0006402	mRNA catabolic process	102	261	1.131e-05
GO:BP	GO:0043065	positive regulation of apoptotic process	183	528	1.145e-05
GO:BP	GO:0030258	lipid modification	81	196	1.270e-05
GO:BP	GO:0051174	regulation of phosphorus metabolic process	306	957	1.298e-05
GO:BP	GO:0031345	negative regulation of cell projection organization	77	184	1.336e-05
GO:BP	GO:0060562	epithelial tube morphogenesis	125	336	1.367e-05
GO:BP	GO:0006109	regulation of carbohydrate metabolic process	74	175	1.367e-05
GO:BP	GO:0006414	translational elongation	41	80	1.416e-05
GO:BP	GO:0042176	regulation of protein catabolic process	135	369	1.424e-05
GO:BP	GO:0031032	actomyosin structure organization	86	212	1.433e-05
GO:BP	GO:0005996	monosaccharide metabolic process	98	250	1.570e-05
GO:BP	GO:0006354	DNA-templated transcription elongation	60	134	1.643e-05
GO:BP	GO:0019220	regulation of phosphate metabolic process	305	956	1.644e-05
GO:BP	GO:0034762	regulation of transmembrane transport	157	443	1.644e-05
GO:BP	GO:1901700	response to oxygen-containing compound	502	1669	1.649e-05
GO:BP	GO:0071363	cellular response to growth factor stimulus	229	689	1.651e-05
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	101	260	1.711e-05
GO:BP	GO:0046032	ADP catabolic process	47	97	1.719e-05
GO:BP	GO:0030111	regulation of Wnt signaling pathway	123	331	1.744e-05
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	85	210	1.809e-05
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	49	103	1.960e-05
GO:BP	GO:0007264	small GTPase-mediated signal transduction	175	505	1.960e-05
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	56	123	1.960e-05
GO:BP	GO:0030488	tRNA methylation	25	40	1.974e-05
GO:BP	GO:0050807	regulation of synapse organization	116	309	1.974e-05
GO:BP	GO:0043068	positive regulation of programmed cell death	187	546	1.986e-05
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	58	129	2.047e-05
GO:BP	GO:0007005	mitochondrion organization	154	435	2.174e-05
GO:BP	GO:0006096	glycolytic process	46	95	2.247e-05
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	119	320	2.453e-05
GO:BP	GO:0019216	regulation of lipid metabolic process	119	320	2.453e-05
GO:BP	GO:0051640	organelle localization	208	620	2.514e-05
GO:BP	GO:0006090	pyruvate metabolic process	56	124	2.619e-05
GO:BP	GO:0045927	positive regulation of growth	99	256	2.676e-05
GO:BP	GO:0046031	ADP metabolic process	49	104	2.714e-05
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	98	253	2.766e-05
GO:BP	GO:1903008	organelle disassembly	37	71	2.771e-05
GO:BP	GO:0019693	ribose phosphate metabolic process	137	380	2.771e-05
GO:BP	GO:0051248	negative regulation of protein metabolic process	224	677	2.985e-05
GO:BP	GO:1901888	regulation of cell junction assembly	101	263	2.985e-05
GO:BP	GO:0042326	negative regulation of phosphorylation	100	260	3.100e-05
GO:BP	GO:0009150	purine ribonucleotide metabolic process	128	351	3.112e-05
GO:BP	GO:0060173	limb development	79	194	3.150e-05
GO:BP	GO:0048736	appendage development	79	194	3.150e-05
GO:BP	GO:0032787	monocarboxylic acid metabolic process	206	616	3.514e-05
GO:BP	GO:0001933	negative regulation of protein phosphorylation	95	245	3.724e-05
GO:BP	GO:0050803	regulation of synapse structure or activity	117	316	3.726e-05
GO:BP	GO:0009259	ribonucleotide metabolic process	134	372	3.728e-05
GO:BP	GO:0046165	alcohol biosynthetic process	62	143	3.733e-05
GO:BP	GO:0072344	rescue of stalled ribosome	22	34	3.733e-05
GO:BP	GO:0010881	regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion	16	21	3.945e-05
GO:BP	GO:0070252	actin-mediated cell contraction	51	111	4.029e-05
GO:BP	GO:0048638	regulation of developmental growth	115	310	4.029e-05
GO:BP	GO:0032535	regulation of cellular component size	129	356	4.029e-05
GO:BP	GO:0032259	methylation	92	236	4.065e-05
GO:BP	GO:0032970	regulation of actin filament-based process	135	376	4.081e-05
GO:BP	GO:0062012	regulation of small molecule metabolic process	118	320	4.137e-05
GO:BP	GO:0001837	epithelial to mesenchymal transition	71	171	4.534e-05
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	56	126	4.564e-05
GO:BP	GO:0009137	purine nucleoside diphosphate catabolic process	47	100	4.583e-05
GO:BP	GO:0009181	purine ribonucleoside diphosphate catabolic process	47	100	4.583e-05
GO:BP	GO:0070585	protein localization to mitochondrion	58	132	4.670e-05
GO:BP	GO:0050890	cognition	120	328	5.256e-05
GO:BP	GO:0006006	glucose metabolic process	75	184	5.312e-05
GO:BP	GO:0043069	negative regulation of programmed cell death	287	905	5.421e-05
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	104	276	5.421e-05
GO:BP	GO:0002009	morphogenesis of an epithelium	172	503	5.540e-05
GO:BP	GO:1903514	release of sequestered calcium ion into cytosol by endoplasmic reticulum	23	37	5.693e-05
GO:BP	GO:1990778	protein localization to cell periphery	131	365	5.753e-05
GO:BP	GO:0051261	protein depolymerization	54	121	5.802e-05
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	296	938	5.856e-05
GO:BP	GO:0032412	regulation of monoatomic ion transmembrane transporter activity	68	163	5.901e-05
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	56	127	5.964e-05
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	46	98	5.967e-05
GO:BP	GO:0016236	macroautophagy	130	362	5.973e-05
GO:BP	GO:0099175	regulation of postsynapse organization	64	151	6.072e-05
GO:BP	GO:0099536	synaptic signaling	259	807	6.096e-05
GO:BP	GO:0050790	regulation of catalytic activity	293	928	6.172e-05
GO:BP	GO:0008015	blood circulation	176	518	6.426e-05
GO:BP	GO:0001944	vasculature development	246	762	6.683e-05
GO:BP	GO:0006486	protein glycosylation	88	226	6.717e-05
GO:BP	GO:0009134	nucleoside diphosphate catabolic process	49	107	6.717e-05
GO:BP	GO:0043413	macromolecule glycosylation	88	226	6.717e-05
GO:BP	GO:0044092	negative regulation of molecular function	186	553	6.894e-05
GO:BP	GO:0019395	fatty acid oxidation	50	110	6.897e-05
GO:BP	GO:0014808	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	22	35	6.971e-05
GO:BP	GO:0009135	purine nucleoside diphosphate metabolic process	52	116	7.241e-05
GO:BP	GO:0009179	purine ribonucleoside diphosphate metabolic process	52	116	7.241e-05
GO:BP	GO:0035108	limb morphogenesis	65	155	7.574e-05
GO:BP	GO:0051494	negative regulation of cytoskeleton organization	65	155	7.574e-05
GO:BP	GO:0035107	appendage morphogenesis	65	155	7.574e-05
GO:BP	GO:0006643	membrane lipid metabolic process	84	214	7.588e-05
GO:BP	GO:0022604	regulation of cell morphogenesis	94	246	7.813e-05
GO:BP	GO:0060070	canonical Wnt signaling pathway	114	311	7.836e-05
GO:BP	GO:0022898	regulation of transmembrane transporter activity	70	171	8.930e-05
GO:BP	GO:0016311	dephosphorylation	85	218	9.003e-05
GO:BP	GO:1901698	response to nitrogen compound	334	1080	9.218e-05
GO:BP	GO:0051963	regulation of synapse assembly	68	165	9.218e-05
GO:BP	GO:0034763	negative regulation of transmembrane transport	51	114	9.403e-05
GO:BP	GO:0034599	cellular response to oxidative stress	94	247	9.403e-05
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	98	260	9.550e-05
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	61	144	9.980e-05
GO:BP	GO:0044093	positive regulation of molecular function	279	884	1.051e-04
GO:BP	GO:0085029	extracellular matrix assembly	27	48	1.052e-04
GO:BP	GO:0016050	vesicle organization	133	376	1.052e-04
GO:BP	GO:0009887	animal organ morphogenesis	323	1042	1.054e-04
GO:BP	GO:0086018	SA node cell to atrial cardiac muscle cell signaling	9	9	1.061e-04
GO:BP	GO:0086015	SA node cell action potential	9	9	1.061e-04
GO:BP	GO:0050801	monoatomic ion homeostasis	203	616	1.077e-04
GO:BP	GO:0001667	ameboidal-type cell migration	90	235	1.085e-04
GO:BP	GO:0009101	glycoprotein biosynthetic process	110	300	1.098e-04
GO:BP	GO:0030334	regulation of cell migration	300	960	1.114e-04
GO:BP	GO:0055080	monoatomic cation homeostasis	200	606	1.124e-04
GO:BP	GO:0019725	cellular homeostasis	265	835	1.124e-04
GO:BP	GO:0007417	central nervous system development	328	1061	1.125e-04
GO:BP	GO:0070085	glycosylation	93	245	1.151e-04
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	112	307	1.166e-04
GO:BP	GO:0030522	intracellular receptor signaling pathway	133	377	1.187e-04
GO:BP	GO:2000145	regulation of cell motility	317	1022	1.187e-04
GO:BP	GO:0044782	cilium organization	149	431	1.187e-04
GO:BP	GO:0043254	regulation of protein-containing complex assembly	146	421	1.213e-04
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	52	118	1.236e-04
GO:BP	GO:0051054	positive regulation of DNA metabolic process	107	291	1.237e-04
GO:BP	GO:0048813	dendrite morphogenesis	61	145	1.237e-04
GO:BP	GO:0045597	positive regulation of cell differentiation	277	879	1.237e-04
GO:BP	GO:0000226	microtubule cytoskeleton organization	218	670	1.237e-04
GO:BP	GO:0046890	regulation of lipid biosynthetic process	73	182	1.239e-04
GO:BP	GO:0032409	regulation of transporter activity	73	182	1.239e-04
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	57	133	1.253e-04
GO:BP	GO:0007610	behavior	219	674	1.293e-04
GO:BP	GO:0009100	glycoprotein metabolic process	131	371	1.293e-04
GO:BP	GO:0034248	regulation of amide metabolic process	34	67	1.306e-04
GO:BP	GO:0040012	regulation of locomotion	329	1067	1.336e-04
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	67	164	1.421e-04
GO:BP	GO:0043066	negative regulation of apoptotic process	275	874	1.490e-04
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	48	107	1.512e-04
GO:BP	GO:1902115	regulation of organelle assembly	89	234	1.591e-04
GO:BP	GO:0048871	multicellular organismal-level homeostasis	261	825	1.631e-04
GO:BP	GO:0141188	nucleic acid catabolic process	122	343	1.776e-04
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	45	99	1.900e-04
GO:BP	GO:0090066	regulation of anatomical structure size	168	500	1.950e-04
GO:BP	GO:0006310	DNA recombination	123	347	1.959e-04
GO:BP	GO:0099537	trans-synaptic signaling	248	781	2.031e-04
GO:BP	GO:0006470	protein dephosphorylation	60	144	2.031e-04
GO:BP	GO:0006913	nucleocytoplasmic transport	119	334	2.059e-04
GO:BP	GO:0051169	nuclear transport	119	334	2.059e-04
GO:BP	GO:0031109	microtubule polymerization or depolymerization	58	138	2.066e-04
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	95	255	2.107e-04
GO:BP	GO:0003205	cardiac chamber development	68	169	2.172e-04
GO:BP	GO:0006338	chromatin remodeling	232	725	2.175e-04
GO:BP	GO:0070296	sarcoplasmic reticulum calcium ion transport	24	42	2.259e-04
GO:BP	GO:0097352	autophagosome maturation	32	63	2.293e-04
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	32	63	2.293e-04
GO:BP	GO:1901879	regulation of protein depolymerization	42	91	2.294e-04
GO:BP	GO:0098657	import into cell	287	922	2.294e-04
GO:BP	GO:0010256	endomembrane system organization	200	613	2.333e-04
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	122	345	2.344e-04
GO:BP	GO:1902904	negative regulation of supramolecular fiber organization	64	157	2.354e-04
GO:BP	GO:0061337	cardiac conduction	43	94	2.366e-04
GO:BP	GO:0007611	learning or memory	103	282	2.378e-04
GO:BP	GO:0009611	response to wounding	187	568	2.429e-04
GO:BP	GO:0048870	cell motility	524	1793	2.498e-04
GO:BP	GO:0007346	regulation of mitotic cell cycle	165	492	2.516e-04
GO:BP	GO:0033673	negative regulation of kinase activity	60	145	2.516e-04
GO:BP	GO:0060271	cilium assembly	139	403	2.529e-04
GO:BP	GO:0016052	carbohydrate catabolic process	69	173	2.568e-04
GO:BP	GO:0010564	regulation of cell cycle process	230	720	2.614e-04
GO:BP	GO:0006979	response to oxidative stress	138	400	2.661e-04
GO:BP	GO:0034329	cell junction assembly	168	503	2.697e-04
GO:BP	GO:0043242	negative regulation of protein-containing complex disassembly	39	83	2.718e-04
GO:BP	GO:0030199	collagen fibril organization	34	69	2.740e-04
GO:BP	GO:0043603	amide metabolic process	154	455	2.768e-04
GO:BP	GO:0006417	regulation of translation	132	380	2.769e-04
GO:BP	GO:0046329	negative regulation of JNK cascade	21	35	2.774e-04
GO:BP	GO:0099068	postsynapse assembly	41	89	2.948e-04
GO:BP	GO:0001568	blood vessel development	233	732	2.948e-04
GO:BP	GO:0031503	protein-containing complex localization	82	215	2.948e-04
GO:BP	GO:0046173	polyol biosynthetic process	31	61	2.951e-04
GO:BP	GO:0007268	chemical synaptic transmission	245	775	3.020e-04
GO:BP	GO:0098916	anterograde trans-synaptic signaling	245	775	3.020e-04
GO:BP	GO:0016477	cell migration	453	1534	3.315e-04
GO:BP	GO:0007017	microtubule-based process	307	999	3.346e-04
GO:BP	GO:0009062	fatty acid catabolic process	47	107	3.383e-04
GO:BP	GO:0055082	intracellular chemical homeostasis	232	730	3.403e-04
GO:BP	GO:0048284	organelle fusion	66	165	3.403e-04
GO:BP	GO:0034440	lipid oxidation	50	116	3.428e-04
GO:BP	GO:0030307	positive regulation of cell growth	65	162	3.487e-04
GO:BP	GO:0006403	RNA localization	77	200	3.545e-04
GO:BP	GO:0007517	muscle organ development	127	365	3.555e-04
GO:BP	GO:0045333	cellular respiration	90	242	3.557e-04
GO:BP	GO:0043647	inositol phosphate metabolic process	24	43	3.583e-04
GO:BP	GO:1901701	cellular response to oxygen-containing compound	357	1182	3.583e-04
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	40	87	3.843e-04
GO:BP	GO:0045214	sarcomere organization	27	51	3.939e-04
GO:BP	GO:0006469	negative regulation of protein kinase activity	57	138	4.139e-04
GO:BP	GO:0010906	regulation of glucose metabolic process	43	96	4.181e-04
GO:BP	GO:0031123	RNA 3’-end processing	43	96	4.181e-04
GO:BP	GO:0010977	negative regulation of neuron projection development	55	132	4.248e-04
GO:BP	GO:0006635	fatty acid beta-oxidation	36	76	4.415e-04
GO:BP	GO:0055007	cardiac muscle cell differentiation	50	117	4.420e-04
GO:BP	GO:0030811	regulation of nucleotide catabolic process	28	54	4.523e-04
GO:BP	GO:0006110	regulation of glycolytic process	28	54	4.523e-04
GO:BP	GO:0033121	regulation of purine nucleotide catabolic process	28	54	4.523e-04
GO:BP	GO:0015931	nucleobase-containing compound transport	88	237	4.587e-04
GO:BP	GO:0010506	regulation of autophagy	127	367	4.619e-04
GO:BP	GO:0042325	regulation of phosphorylation	259	830	4.622e-04
GO:BP	GO:0006739	NADP metabolic process	23	41	4.675e-04
GO:BP	GO:0032868	response to insulin	98	270	4.697e-04
GO:BP	GO:0006360	transcription by RNA polymerase I	34	71	5.490e-04
GO:BP	GO:0098771	inorganic ion homeostasis	175	534	5.598e-04
GO:BP	GO:0022402	cell cycle process	382	1280	5.614e-04
GO:BP	GO:0045732	positive regulation of protein catabolic process	79	209	5.684e-04
GO:BP	GO:0007026	negative regulation of microtubule depolymerization	18	29	5.709e-04
GO:BP	GO:0043062	extracellular structure organization	115	328	5.718e-04
GO:BP	GO:0006487	protein N-linked glycosylation	35	74	5.788e-04
GO:BP	GO:0006066	alcohol metabolic process	125	362	5.857e-04
GO:BP	GO:0006401	RNA catabolic process	111	315	6.091e-04
GO:BP	GO:0051241	negative regulation of multicellular organismal process	329	1087	6.109e-04
GO:BP	GO:0043484	regulation of RNA splicing	72	187	6.186e-04
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	75	197	6.677e-04
GO:BP	GO:0000278	mitotic cell cycle	275	892	6.687e-04
GO:BP	GO:0007416	synapse assembly	94	259	6.687e-04
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	87	236	6.700e-04
GO:BP	GO:0006352	DNA-templated transcription initiation	79	210	6.750e-04
GO:BP	GO:0060322	head development	251	806	6.947e-04
GO:BP	GO:0002027	regulation of heart rate	44	101	7.376e-04
GO:BP	GO:0000724	double-strand break repair via homologous recombination	72	188	7.488e-04
GO:BP	GO:0046467	membrane lipid biosynthetic process	60	150	7.496e-04
GO:BP	GO:0008283	cell population proliferation	578	2015	7.566e-04
GO:BP	GO:0050678	regulation of epithelial cell proliferation	125	364	7.591e-04
GO:BP	GO:0051168	nuclear export	66	169	7.634e-04
GO:BP	GO:0044282	small molecule catabolic process	127	371	7.760e-04
GO:BP	GO:2000377	regulation of reactive oxygen species metabolic process	58	144	7.861e-04
GO:BP	GO:0030198	extracellular matrix organization	114	327	7.879e-04
GO:BP	GO:0061013	regulation of mRNA catabolic process	75	198	7.923e-04
GO:BP	GO:0051236	establishment of RNA localization	64	163	8.130e-04
GO:BP	GO:0010927	cellular component assembly involved in morphogenesis	56	138	8.205e-04
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	56	138	8.205e-04
GO:BP	GO:0050657	nucleic acid transport	63	160	8.327e-04
GO:BP	GO:0050658	RNA transport	63	160	8.327e-04
GO:BP	GO:0140694	membraneless organelle assembly	144	430	8.327e-04
GO:BP	GO:0001503	ossification	144	430	8.327e-04
GO:BP	GO:0030162	regulation of proteolysis	137	406	8.420e-04
GO:BP	GO:0072659	protein localization to plasma membrane	103	291	9.018e-04
GO:BP	GO:0048598	embryonic morphogenesis	198	620	9.181e-04
GO:BP	GO:0097190	apoptotic signaling pathway	194	606	9.325e-04
GO:BP	GO:0001947	heart looping	32	67	9.384e-04
GO:BP	GO:0061157	mRNA destabilization	44	102	9.470e-04
GO:BP	GO:0051348	negative regulation of transferase activity	65	167	9.515e-04
GO:BP	GO:0008361	regulation of cell size	70	183	9.578e-04
GO:BP	GO:0048511	rhythmic process	107	305	9.731e-04
GO:BP	GO:0048639	positive regulation of developmental growth	64	164	9.808e-04
GO:BP	GO:0009303	rRNA transcription	22	40	9.808e-04
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	129	380	1.004e-03
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	109	312	1.005e-03
GO:BP	GO:0010765	positive regulation of sodium ion transport	18	30	1.010e-03
GO:BP	GO:0000725	recombinational repair	73	193	1.014e-03
GO:BP	GO:0045229	external encapsulating structure organization	114	329	1.014e-03
GO:BP	GO:0003143	embryonic heart tube morphogenesis	34	73	1.024e-03
GO:BP	GO:1901880	negative regulation of protein depolymerization	34	73	1.024e-03
GO:BP	GO:0000460	maturation of 5.8S rRNA	20	35	1.024e-03
GO:BP	GO:0031114	regulation of microtubule depolymerization	20	35	1.024e-03
GO:BP	GO:0030048	actin filament-based movement	55	136	1.024e-03
GO:BP	GO:0046034	ATP metabolic process	84	229	1.036e-03
GO:BP	GO:0007033	vacuole organization	87	239	1.058e-03
GO:BP	GO:0006740	NADPH regeneration	15	23	1.086e-03
GO:BP	GO:0003206	cardiac chamber morphogenesis	51	124	1.115e-03
GO:BP	GO:0050804	modulation of chemical synaptic transmission	167	513	1.133e-03
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	124	364	1.139e-03
GO:BP	GO:0043488	regulation of mRNA stability	69	181	1.182e-03
GO:BP	GO:0060627	regulation of vesicle-mediated transport	172	531	1.185e-03
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	170	524	1.187e-03
GO:BP	GO:0110053	regulation of actin filament organization	94	263	1.193e-03
GO:BP	GO:0050779	RNA destabilization	45	106	1.193e-03
GO:BP	GO:0006664	glycolipid metabolic process	45	106	1.193e-03
GO:BP	GO:2000779	regulation of double-strand break repair	57	143	1.197e-03
GO:BP	GO:0006897	endocytosis	222	709	1.231e-03
GO:BP	GO:0099177	regulation of trans-synaptic signaling	167	514	1.248e-03
GO:BP	GO:0035567	non-canonical Wnt signaling pathway	32	68	1.275e-03
GO:BP	GO:0030100	regulation of endocytosis	104	297	1.275e-03
GO:BP	GO:0050684	regulation of mRNA processing	54	134	1.295e-03
GO:BP	GO:0099003	vesicle-mediated transport in synapse	92	257	1.309e-03
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	66	172	1.313e-03
GO:BP	GO:0051258	protein polymerization	100	284	1.358e-03
GO:BP	GO:1905037	autophagosome organization	51	125	1.387e-03
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	172	533	1.443e-03
GO:BP	GO:0051926	negative regulation of calcium ion transport	29	60	1.499e-03
GO:BP	GO:0006289	nucleotide-excision repair	37	83	1.501e-03
GO:BP	GO:0031669	cellular response to nutrient levels	89	248	1.516e-03
GO:BP	GO:0031111	negative regulation of microtubule polymerization or depolymerization	22	41	1.516e-03
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	95	268	1.516e-03
GO:BP	GO:1903509	liposaccharide metabolic process	45	107	1.521e-03
GO:BP	GO:0006626	protein targeting to mitochondrion	44	104	1.532e-03
GO:BP	GO:0048193	Golgi vesicle transport	108	312	1.553e-03
GO:BP	GO:0001654	eye development	138	415	1.571e-03
GO:BP	GO:0003229	ventricular cardiac muscle tissue development	30	63	1.584e-03
GO:BP	GO:0060561	apoptotic process involved in morphogenesis	16	26	1.623e-03
GO:BP	GO:0030335	positive regulation of cell migration	179	559	1.626e-03
GO:BP	GO:0060429	epithelium development	366	1238	1.654e-03
GO:BP	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	31	66	1.669e-03
GO:BP	GO:0035051	cardiocyte differentiation	59	151	1.679e-03
GO:BP	GO:0006506	GPI anchor biosynthetic process	18	31	1.708e-03
GO:BP	GO:0034612	response to tumor necrosis factor	83	229	1.726e-03
GO:BP	GO:0043487	regulation of RNA stability	72	193	1.743e-03
GO:BP	GO:0009225	nucleotide-sugar metabolic process	23	44	1.743e-03
GO:BP	GO:1903170	negative regulation of calcium ion transmembrane transport	23	44	1.743e-03
GO:BP	GO:0051050	positive regulation of transport	259	847	1.774e-03
GO:BP	GO:0032886	regulation of microtubule-based process	94	266	1.821e-03
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	117	344	1.830e-03
GO:BP	GO:0043086	negative regulation of catalytic activity	102	293	1.833e-03
GO:BP	GO:0048514	blood vessel morphogenesis	200	635	1.833e-03
GO:BP	GO:0042752	regulation of circadian rhythm	47	114	1.854e-03
GO:BP	GO:0050673	epithelial cell proliferation	145	441	1.869e-03
GO:BP	GO:0030308	negative regulation of cell growth	66	174	1.870e-03
GO:BP	GO:0007368	determination of left/right symmetry	55	139	1.889e-03
GO:BP	GO:0140352	export from cell	281	928	1.897e-03
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	45	108	1.903e-03
GO:BP	GO:0007623	circadian rhythm	77	210	1.928e-03
GO:BP	GO:0043467	regulation of generation of precursor metabolites and energy	54	136	1.940e-03
GO:BP	GO:0140238	presynaptic endocytosis	38	87	1.958e-03
GO:BP	GO:0043269	regulation of monoatomic ion transport	148	452	1.965e-03
GO:BP	GO:0051093	negative regulation of developmental process	280	925	1.979e-03
GO:BP	GO:0006874	intracellular calcium ion homeostasis	105	304	2.034e-03
GO:BP	GO:0051028	mRNA transport	52	130	2.048e-03
GO:BP	GO:0060998	regulation of dendritic spine development	29	61	2.049e-03
GO:BP	GO:0050679	positive regulation of epithelial cell proliferation	75	204	2.107e-03
GO:BP	GO:0006839	mitochondrial transport	67	178	2.128e-03
GO:BP	GO:0006734	NADH metabolic process	19	34	2.128e-03
GO:BP	GO:0006812	monoatomic cation transport	319	1069	2.145e-03
GO:BP	GO:0060972	left/right pattern formation	57	146	2.145e-03
GO:BP	GO:0043470	regulation of carbohydrate catabolic process	30	64	2.149e-03
GO:BP	GO:0071985	multivesicular body sorting pathway	25	50	2.155e-03
GO:BP	GO:1903047	mitotic cell cycle process	230	745	2.198e-03
GO:BP	GO:0030001	metal ion transport	268	883	2.237e-03
GO:BP	GO:0000045	autophagosome assembly	48	118	2.245e-03
GO:BP	GO:0086070	SA node cell to atrial cardiac muscle cell communication	9	11	2.259e-03
GO:BP	GO:0048251	elastic fiber assembly	9	11	2.259e-03
GO:BP	GO:0001941	postsynaptic membrane organization	22	42	2.259e-03
GO:BP	GO:0099504	synaptic vesicle cycle	80	221	2.266e-03
GO:BP	GO:0051960	regulation of nervous system development	149	457	2.271e-03
GO:BP	GO:0071897	DNA biosynthetic process	65	172	2.283e-03
GO:BP	GO:0045444	fat cell differentiation	86	241	2.283e-03
GO:BP	GO:1901699	cellular response to nitrogen compound	202	645	2.298e-03
GO:BP	GO:0030490	maturation of SSU-rRNA	26	53	2.329e-03
GO:BP	GO:0061371	determination of heart left/right asymmetry	33	73	2.362e-03
GO:BP	GO:0150063	visual system development	138	419	2.366e-03
GO:BP	GO:0043434	response to peptide hormone	144	440	2.380e-03
GO:BP	GO:0010959	regulation of metal ion transport	125	374	2.390e-03
GO:BP	GO:0140056	organelle localization by membrane tethering	34	76	2.405e-03
GO:BP	GO:0050773	regulation of dendrite development	42	100	2.450e-03
GO:BP	GO:0043536	positive regulation of blood vessel endothelial cell migration	27	56	2.491e-03
GO:BP	GO:0046364	monosaccharide biosynthetic process	39	91	2.491e-03
GO:BP	GO:0141137	positive regulation of gene expression, epigenetic	27	56	2.491e-03
GO:BP	GO:0060314	regulation of ryanodine-sensitive calcium-release channel activity	14	22	2.494e-03
GO:BP	GO:0009895	negative regulation of catabolic process	121	361	2.625e-03
GO:BP	GO:0032271	regulation of protein polymerization	73	199	2.664e-03
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	49	122	2.689e-03
GO:BP	GO:0180046	GPI anchored protein biosynthesis	18	32	2.733e-03
GO:BP	GO:0006505	GPI anchor metabolic process	18	32	2.733e-03
GO:BP	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	18	32	2.733e-03
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	113	334	2.791e-03
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	54	138	2.840e-03
GO:BP	GO:0048675	axon extension	46	113	2.873e-03
GO:BP	GO:0016054	organic acid catabolic process	87	246	2.873e-03
GO:BP	GO:0046395	carboxylic acid catabolic process	87	246	2.873e-03
GO:BP	GO:0043271	negative regulation of monoatomic ion transport	46	113	2.873e-03
GO:BP	GO:2000147	positive regulation of cell motility	185	587	2.892e-03
GO:BP	GO:1905475	regulation of protein localization to membrane	71	193	2.892e-03
GO:BP	GO:0032940	secretion by cell	259	854	2.892e-03
GO:BP	GO:1903115	regulation of actin filament-based movement	21	40	2.925e-03
GO:BP	GO:0000209	protein polyubiquitination	97	280	2.985e-03
GO:BP	GO:0042180	ketone metabolic process	77	213	2.997e-03
GO:BP	GO:0034765	regulation of monoatomic ion transmembrane transport	109	321	3.021e-03
GO:BP	GO:0035265	organ growth	62	164	3.030e-03
GO:BP	GO:0008285	negative regulation of cell population proliferation	218	706	3.030e-03
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	66	177	3.043e-03
GO:BP	GO:0009855	determination of bilateral symmetry	57	148	3.056e-03
GO:BP	GO:0060996	dendritic spine development	42	101	3.056e-03
GO:BP	GO:0009799	specification of symmetry	57	148	3.056e-03
GO:BP	GO:0038127	ERBB signaling pathway	51	129	3.076e-03
GO:BP	GO:0036465	synaptic vesicle recycling	40	95	3.129e-03
GO:BP	GO:0046620	regulation of organ growth	38	89	3.162e-03
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	65	174	3.162e-03
GO:BP	GO:0048488	synaptic vesicle endocytosis	36	83	3.162e-03
GO:BP	GO:0055006	cardiac cell development	37	86	3.162e-03
GO:BP	GO:0072329	monocarboxylic acid catabolic process	50	126	3.162e-03
GO:BP	GO:0031667	response to nutrient levels	163	510	3.183e-03
GO:BP	GO:0090174	organelle membrane fusion	49	123	3.246e-03
GO:BP	GO:0032869	cellular response to insulin stimulus	75	207	3.250e-03
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	55	142	3.257e-03
GO:BP	GO:0060999	positive regulation of dendritic spine development	22	43	3.259e-03
GO:BP	GO:0030155	regulation of cell adhesion	242	794	3.259e-03
GO:BP	GO:0040017	positive regulation of locomotion	189	603	3.301e-03
GO:BP	GO:0048880	sensory system development	139	426	3.335e-03
GO:BP	GO:0006887	exocytosis	120	360	3.390e-03
GO:BP	GO:0060491	regulation of cell projection assembly	74	204	3.392e-03
GO:BP	GO:0000165	MAPK cascade	228	744	3.455e-03
GO:BP	GO:0042391	regulation of membrane potential	148	458	3.474e-03
GO:BP	GO:0046039	GTP metabolic process	15	25	3.476e-03
GO:BP	GO:0048668	collateral sprouting	17	30	3.478e-03
GO:BP	GO:0072593	reactive oxygen species metabolic process	82	231	3.602e-03
GO:BP	GO:0070588	calcium ion transmembrane transport	114	340	3.686e-03
GO:BP	GO:0006816	calcium ion transport	141	434	3.690e-03
GO:BP	GO:0036293	response to decreased oxygen levels	107	316	3.717e-03
GO:BP	GO:0071356	cellular response to tumor necrosis factor	75	208	3.769e-03
GO:BP	GO:0055085	transmembrane transport	453	1578	3.890e-03
GO:BP	GO:0048863	stem cell differentiation	86	245	3.915e-03
GO:BP	GO:0042181	ketone biosynthetic process	24	49	3.932e-03
GO:BP	GO:0010594	regulation of endothelial cell migration	63	169	4.050e-03
GO:BP	GO:0019319	hexose biosynthetic process	37	87	4.050e-03
GO:BP	GO:0006094	gluconeogenesis	36	84	4.057e-03
GO:BP	GO:0034766	negative regulation of monoatomic ion transmembrane transport	36	84	4.057e-03
GO:BP	GO:0006906	vesicle fusion	48	121	4.073e-03
GO:BP	GO:0016051	carbohydrate biosynthetic process	70	192	4.077e-03
GO:BP	GO:0120032	regulation of plasma membrane bounded cell projection assembly	73	202	4.135e-03
GO:BP	GO:0007030	Golgi organization	58	153	4.174e-03
GO:BP	GO:0071887	leukocyte apoptotic process	47	118	4.183e-03
GO:BP	GO:0045445	myoblast differentiation	46	115	4.304e-03
GO:BP	GO:0022904	respiratory electron transport chain	46	115	4.304e-03
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	57	150	4.335e-03
GO:BP	GO:0061008	hepaticobiliary system development	57	150	4.335e-03
GO:BP	GO:0032204	regulation of telomere maintenance	45	112	4.415e-03
GO:BP	GO:0000479	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	11	16	4.501e-03
GO:BP	GO:0006811	monoatomic ion transport	373	1282	4.619e-03
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	43	106	4.644e-03
GO:BP	GO:0016073	snRNA metabolic process	27	58	4.649e-03
GO:BP	GO:0048732	gland development	146	454	4.667e-03
GO:BP	GO:0043010	camera-type eye development	120	363	4.707e-03
GO:BP	GO:0042060	wound healing	140	433	4.726e-03
GO:BP	GO:0038202	TORC1 signaling	42	103	4.729e-03
GO:BP	GO:1904062	regulation of monoatomic cation transmembrane transport	97	284	4.864e-03
GO:BP	GO:0033135	regulation of peptidyl-serine phosphorylation	40	97	4.926e-03
GO:BP	GO:0006301	postreplication repair	19	36	4.971e-03
GO:BP	GO:0106027	neuron projection organization	39	94	5.004e-03
GO:BP	GO:0042127	regulation of cell population proliferation	480	1685	5.101e-03
GO:BP	GO:0098655	monoatomic cation transmembrane transport	263	877	5.111e-03
GO:BP	GO:0043534	blood vessel endothelial cell migration	47	119	5.117e-03
GO:BP	GO:0003208	cardiac ventricle morphogenesis	31	70	5.122e-03
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	31	70	5.122e-03
GO:BP	GO:1902116	negative regulation of organelle assembly	23	47	5.129e-03
GO:BP	GO:0045661	regulation of myoblast differentiation	33	76	5.197e-03
GO:BP	GO:0090153	regulation of sphingolipid biosynthetic process	10	14	5.232e-03
GO:BP	GO:0009892	negative regulation of metabolic process	922	3375	5.232e-03
GO:BP	GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation	10	14	5.232e-03
GO:BP	GO:0007006	mitochondrial membrane organization	46	116	5.232e-03
GO:BP	GO:0015780	nucleotide-sugar transmembrane transport	10	14	5.232e-03
GO:BP	GO:0051259	protein complex oligomerization	93	271	5.232e-03
GO:BP	GO:0001932	regulation of protein phosphorylation	236	779	5.299e-03
GO:BP	GO:0014074	response to purine-containing compound	56	148	5.332e-03
GO:BP	GO:0046683	response to organophosphorus	51	132	5.383e-03
GO:BP	GO:0098815	modulation of excitatory postsynaptic potential	24	50	5.455e-03
GO:BP	GO:0007420	brain development	229	754	5.486e-03
GO:BP	GO:0048568	embryonic organ development	148	463	5.548e-03
GO:BP	GO:0010976	positive regulation of neuron projection development	59	158	5.591e-03
GO:BP	GO:0045912	negative regulation of carbohydrate metabolic process	25	53	5.771e-03
GO:BP	GO:0072033	renal vesicle formation	7	8	5.791e-03
GO:BP	GO:0018202	peptidyl-histidine modification	7	8	5.791e-03
GO:BP	GO:0022038	corpus callosum development	15	26	5.834e-03
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	109	327	5.908e-03
GO:BP	GO:0045926	negative regulation of growth	80	228	5.964e-03
GO:BP	GO:0086065	cell communication involved in cardiac conduction	26	56	6.014e-03
GO:BP	GO:0051651	maintenance of location in cell	74	208	6.061e-03
GO:BP	GO:0007032	endosome organization	40	98	6.083e-03
GO:BP	GO:1904861	excitatory synapse assembly	21	42	6.177e-03
GO:BP	GO:0055008	cardiac muscle tissue morphogenesis	27	59	6.211e-03
GO:BP	GO:0071559	response to transforming growth factor beta	92	269	6.211e-03
GO:BP	GO:0031125	rRNA 3’-end processing	8	10	6.220e-03
GO:BP	GO:0060541	respiratory system development	79	225	6.245e-03
GO:BP	GO:0046889	positive regulation of lipid biosynthetic process	38	92	6.301e-03
GO:BP	GO:1904375	regulation of protein localization to cell periphery	56	149	6.315e-03
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	326	1113	6.325e-03
GO:BP	GO:0007015	actin filament organization	147	461	6.370e-03
GO:BP	GO:0043543	protein acylation	37	89	6.382e-03
GO:BP	GO:0048814	regulation of dendrite morphogenesis	29	65	6.455e-03
GO:BP	GO:0022406	membrane docking	36	86	6.455e-03
GO:BP	GO:0062207	regulation of pattern recognition receptor signaling pathway	63	172	6.455e-03
GO:BP	GO:0040011	locomotion	364	1255	6.519e-03
GO:BP	GO:0060419	heart growth	35	83	6.519e-03
GO:BP	GO:0032006	regulation of TOR signaling	55	146	6.541e-03
GO:BP	GO:1903578	regulation of ATP metabolic process	32	74	6.600e-03
GO:BP	GO:0007007	inner mitochondrial membrane organization	22	45	6.623e-03
GO:BP	GO:0018279	protein N-linked glycosylation via asparagine	22	45	6.623e-03
GO:BP	GO:0031589	cell-substrate adhesion	117	356	6.643e-03
GO:BP	GO:0009725	response to hormone	270	907	6.643e-03
GO:BP	GO:0042594	response to starvation	77	219	6.832e-03
GO:BP	GO:0051648	vesicle localization	77	219	6.832e-03
GO:BP	GO:0009060	aerobic respiration	71	199	6.925e-03
GO:BP	GO:0110154	RNA decapping	12	19	7.010e-03
GO:BP	GO:0018205	peptidyl-lysine modification	53	140	7.075e-03
GO:BP	GO:0043500	muscle adaptation	42	105	7.075e-03
GO:BP	GO:1990823	response to leukemia inhibitory factor	42	105	7.075e-03
GO:BP	GO:0009649	entrainment of circadian clock	16	29	7.107e-03
GO:BP	GO:0051156	glucose 6-phosphate metabolic process	16	29	7.107e-03
GO:BP	GO:0007219	Notch signaling pathway	67	186	7.214e-03
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	67	186	7.214e-03
GO:BP	GO:0055074	calcium ion homeostasis	109	329	7.246e-03
GO:BP	GO:0045739	positive regulation of DNA repair	52	137	7.336e-03
GO:BP	GO:0007423	sensory organ development	192	624	7.381e-03
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	14	24	7.444e-03
GO:BP	GO:1903432	regulation of TORC1 signaling	39	96	7.616e-03
GO:BP	GO:0001889	liver development	55	147	7.727e-03
GO:BP	GO:0016042	lipid catabolic process	116	354	7.759e-03
GO:BP	GO:0043535	regulation of blood vessel endothelial cell migration	38	93	7.777e-03
GO:BP	GO:0030097	hemopoiesis	288	976	7.816e-03
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	62	170	7.816e-03
GO:BP	GO:0048754	branching morphogenesis of an epithelial tube	58	157	8.000e-03
GO:BP	GO:0035050	embryonic heart tube development	36	87	8.074e-03
GO:BP	GO:0051924	regulation of calcium ion transport	84	244	8.104e-03
GO:BP	GO:1901873	regulation of post-translational protein modification	84	244	8.104e-03
GO:BP	GO:0010038	response to metal ion	115	351	8.133e-03
GO:BP	GO:0031929	TOR signaling	61	167	8.133e-03
GO:BP	GO:0010810	regulation of cell-substrate adhesion	76	217	8.133e-03
GO:BP	GO:1903169	regulation of calcium ion transmembrane transport	61	167	8.133e-03
GO:BP	GO:0061448	connective tissue development	98	292	8.133e-03
GO:BP	GO:0060420	regulation of heart growth	27	60	8.133e-03
GO:BP	GO:1901019	regulation of calcium ion transmembrane transporter activity	27	60	8.133e-03
GO:BP	GO:0086001	cardiac muscle cell action potential	34	81	8.224e-03
GO:BP	GO:0086003	cardiac muscle cell contraction	34	81	8.224e-03
GO:BP	GO:0099022	vesicle tethering	17	32	8.300e-03
GO:BP	GO:0010212	response to ionizing radiation	53	141	8.303e-03
GO:BP	GO:0010632	regulation of epithelial cell migration	29	66	8.314e-03
GO:BP	GO:0007155	cell adhesion	436	1530	8.319e-03
GO:BP	GO:0071901	negative regulation of protein serine/threonine kinase activity	31	72	8.357e-03
GO:BP	GO:0042221	response to chemical	1056	3909	8.375e-03
GO:BP	GO:0034220	monoatomic ion transmembrane transport	307	1048	8.541e-03
GO:BP	GO:0043649	dicarboxylic acid catabolic process	11	17	8.607e-03
GO:BP	GO:0007224	smoothened signaling pathway	56	151	8.607e-03
GO:BP	GO:1901096	regulation of autophagosome maturation	11	17	8.607e-03
GO:BP	GO:0090205	positive regulation of cholesterol metabolic process	11	17	8.607e-03
GO:BP	GO:2001235	positive regulation of apoptotic signaling pathway	52	138	8.607e-03
GO:BP	GO:0150115	cell-substrate junction organization	41	103	8.773e-03
GO:BP	GO:1990830	cellular response to leukemia inhibitory factor	41	103	8.773e-03
GO:BP	GO:0007411	axon guidance	82	238	8.839e-03
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	89	262	8.970e-03
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	62	171	8.971e-03
GO:BP	GO:1990138	neuron projection extension	62	171	8.971e-03
GO:BP	GO:0039531	regulation of cytoplasmic pattern recognition receptor signaling pathway	46	119	9.049e-03
GO:BP	GO:0033137	negative regulation of peptidyl-serine phosphorylation	15	27	9.138e-03
GO:BP	GO:0009226	nucleotide-sugar biosynthetic process	15	27	9.138e-03
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	104	314	9.198e-03
GO:BP	GO:0051235	maintenance of location	76	218	9.198e-03
GO:BP	GO:0016180	snRNA processing	18	35	9.315e-03
GO:BP	GO:0046320	regulation of fatty acid oxidation	18	35	9.315e-03
GO:BP	GO:0050775	positive regulation of dendrite morphogenesis	18	35	9.315e-03
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	18	35	9.315e-03
GO:BP	GO:0034312	diol biosynthetic process	13	22	9.393e-03
GO:BP	GO:0035493	SNARE complex assembly	13	22	9.393e-03
GO:BP	GO:0006390	mitochondrial transcription	13	22	9.393e-03
GO:BP	GO:0016197	endosomal transport	97	290	9.393e-03
GO:BP	GO:1900407	regulation of cellular response to oxidative stress	13	22	9.393e-03
GO:BP	GO:0098662	inorganic cation transmembrane transport	254	854	9.414e-03
GO:BP	GO:0071526	semaphorin-plexin signaling pathway	23	49	9.447e-03
GO:BP	GO:0006497	protein lipidation	23	49	9.447e-03
GO:BP	GO:0007613	memory	49	129	9.591e-03
GO:BP	GO:0048872	homeostasis of number of cells	109	332	9.733e-03
GO:BP	GO:0000959	mitochondrial RNA metabolic process	24	52	9.841e-03
GO:BP	GO:0007254	JNK cascade	63	175	9.849e-03
GO:BP	GO:0097485	neuron projection guidance	82	239	9.912e-03
GO:BP	GO:0022900	electron transport chain	48	126	9.972e-03
GO:BP	GO:0001890	placenta development	56	152	9.977e-03
GO:BP	GO:2001257	regulation of cation channel activity	35	85	9.988e-03
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	102	308	1.009e-02
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	104	315	1.014e-02
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	71	202	1.020e-02
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	19	38	1.021e-02
GO:BP	GO:0010595	positive regulation of endothelial cell migration	42	107	1.022e-02
GO:BP	GO:0071248	cellular response to metal ion	68	192	1.028e-02
GO:BP	GO:1903829	positive regulation of protein localization	156	499	1.029e-02
GO:BP	GO:0043462	regulation of ATP-dependent activity	27	61	1.044e-02
GO:BP	GO:0051284	positive regulation of sequestering of calcium ion	10	15	1.045e-02
GO:BP	GO:0072175	epithelial tube formation	51	136	1.045e-02
GO:BP	GO:0031113	regulation of microtubule polymerization	28	64	1.051e-02
GO:BP	GO:0090130	tissue migration	41	104	1.052e-02
GO:BP	GO:0044772	mitotic cell cycle phase transition	136	428	1.056e-02
GO:BP	GO:0046856	phosphatidylinositol dephosphorylation	16	30	1.063e-02
GO:BP	GO:0000302	response to reactive oxygen species	70	199	1.065e-02
GO:BP	GO:0061387	regulation of extent of cell growth	40	101	1.084e-02
GO:BP	GO:0006631	fatty acid metabolic process	128	400	1.091e-02
GO:BP	GO:0032509	endosome transport via multivesicular body sorting pathway	20	41	1.100e-02
GO:BP	GO:0001666	response to hypoxia	100	302	1.112e-02
GO:BP	GO:0070482	response to oxygen levels	112	344	1.129e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	63	176	1.132e-02
GO:BP	GO:0001525	angiogenesis	169	547	1.141e-02
GO:BP	GO:0003231	cardiac ventricle development	48	127	1.186e-02
GO:BP	GO:0032870	cellular response to hormone stimulus	194	638	1.189e-02
GO:BP	GO:0006098	pentose-phosphate shunt	12	20	1.205e-02
GO:BP	GO:0033194	response to hydroperoxide	12	20	1.205e-02
GO:BP	GO:0031116	positive regulation of microtubule polymerization	17	33	1.212e-02
GO:BP	GO:2000463	positive regulation of excitatory postsynaptic potential	17	33	1.212e-02
GO:BP	GO:0060421	positive regulation of heart growth	17	33	1.212e-02
GO:BP	GO:0070201	regulation of establishment of protein localization	166	537	1.215e-02
GO:BP	GO:0007269	neurotransmitter secretion	55	150	1.215e-02
GO:BP	GO:0099643	signal release from synapse	55	150	1.215e-02
GO:BP	GO:0034097	response to cytokine	278	947	1.223e-02
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	22	47	1.225e-02
GO:BP	GO:0051962	positive regulation of nervous system development	98	296	1.227e-02
GO:BP	GO:0051402	neuron apoptotic process	98	296	1.227e-02
GO:BP	GO:0007612	learning	58	160	1.231e-02
GO:BP	GO:0019827	stem cell population maintenance	64	180	1.240e-02
GO:BP	GO:1902817	negative regulation of protein localization to microtubule	5	5	1.248e-02
GO:BP	GO:1902816	regulation of protein localization to microtubule	5	5	1.248e-02
GO:BP	GO:0086046	membrane depolarization during SA node cell action potential	5	5	1.248e-02
GO:BP	GO:0019042	viral latency	5	5	1.248e-02
GO:BP	GO:0097114	NMDA glutamate receptor clustering	5	5	1.248e-02
GO:BP	GO:0097061	dendritic spine organization	34	83	1.250e-02
GO:BP	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	9	13	1.250e-02
GO:BP	GO:2000303	regulation of ceramide biosynthetic process	9	13	1.250e-02
GO:BP	GO:0090481	pyrimidine nucleotide-sugar transmembrane transport	9	13	1.250e-02
GO:BP	GO:0007019	microtubule depolymerization	23	50	1.258e-02
GO:BP	GO:0009267	cellular response to starvation	63	177	1.294e-02
GO:BP	GO:0045815	transcription initiation-coupled chromatin remodeling	24	53	1.294e-02
GO:BP	GO:0009247	glycolipid biosynthetic process	32	77	1.295e-02
GO:BP	GO:0007389	pattern specification process	149	477	1.313e-02
GO:BP	GO:1901987	regulation of cell cycle phase transition	135	427	1.313e-02
GO:BP	GO:0010718	positive regulation of epithelial to mesenchymal transition	25	56	1.317e-02
GO:BP	GO:0043542	endothelial cell migration	76	221	1.317e-02
GO:BP	GO:0045667	regulation of osteoblast differentiation	49	131	1.326e-02
GO:BP	GO:0051145	smooth muscle cell differentiation	28	65	1.339e-02
GO:BP	GO:0006383	transcription by RNA polymerase III	27	62	1.339e-02
GO:BP	GO:0098727	maintenance of cell number	65	184	1.346e-02
GO:BP	GO:0000723	telomere maintenance	59	164	1.350e-02
GO:BP	GO:0104004	cellular response to environmental stimulus	110	339	1.359e-02
GO:BP	GO:0071214	cellular response to abiotic stimulus	110	339	1.359e-02
GO:BP	GO:0072001	renal system development	108	332	1.360e-02
GO:BP	GO:0032386	regulation of intracellular transport	89	266	1.382e-02
GO:BP	GO:0008154	actin polymerization or depolymerization	67	191	1.396e-02
GO:BP	GO:0033044	regulation of chromosome organization	82	242	1.396e-02
GO:BP	GO:0097553	calcium ion transmembrane import into cytosol	64	181	1.412e-02
GO:BP	GO:0060323	head morphogenesis	19	39	1.424e-02
GO:BP	GO:0043085	positive regulation of catalytic activity	170	554	1.466e-02
GO:BP	GO:0035148	tube formation	54	148	1.468e-02
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	81	239	1.473e-02
GO:BP	GO:0043409	negative regulation of MAPK cascade	57	158	1.486e-02
GO:BP	GO:0006665	sphingolipid metabolic process	60	168	1.491e-02
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	20	42	1.511e-02
GO:BP	GO:1901652	response to peptide	281	962	1.511e-02
GO:BP	GO:0001501	skeletal system development	166	540	1.511e-02
GO:BP	GO:0045540	regulation of cholesterol biosynthetic process	13	23	1.511e-02
GO:BP	GO:0106118	regulation of sterol biosynthetic process	13	23	1.511e-02
GO:BP	GO:0046519	sphingoid metabolic process	13	23	1.511e-02
GO:BP	GO:1905038	regulation of membrane lipid metabolic process	11	18	1.512e-02
GO:BP	GO:0006743	ubiquinone metabolic process	11	18	1.512e-02
GO:BP	GO:0046903	secretion	289	992	1.529e-02
GO:BP	GO:0097107	postsynaptic density assembly	16	31	1.566e-02
GO:BP	GO:0034311	diol metabolic process	16	31	1.566e-02
GO:BP	GO:0046209	nitric oxide metabolic process	33	81	1.573e-02
GO:BP	GO:1903573	negative regulation of response to endoplasmic reticulum stress	21	45	1.573e-02
GO:BP	GO:0046622	positive regulation of organ growth	21	45	1.573e-02
GO:BP	GO:0061001	regulation of dendritic spine morphogenesis	21	45	1.573e-02
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	52	142	1.597e-02
GO:BP	GO:0051147	regulation of muscle cell differentiation	52	142	1.597e-02
GO:BP	GO:0000480	endonucleolytic cleavage in 5’-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	6	7	1.614e-02
GO:BP	GO:0060710	chorio-allantoic fusion	6	7	1.614e-02
GO:BP	GO:0045834	positive regulation of lipid metabolic process	48	129	1.614e-02
GO:BP	GO:0097680	double-strand break repair via classical nonhomologous end joining	7	9	1.614e-02
GO:BP	GO:0048033	heme O metabolic process	7	9	1.614e-02
GO:BP	GO:0017183	protein histidyl modification to diphthamide	6	7	1.614e-02
GO:BP	GO:0014883	transition between fast and slow fiber	6	7	1.614e-02
GO:BP	GO:0048034	heme O biosynthetic process	7	9	1.614e-02
GO:BP	GO:0000467	exonucleolytic trimming to generate mature 3’-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	7	9	1.614e-02
GO:BP	GO:0043604	amide biosynthetic process	61	172	1.614e-02
GO:BP	GO:0032206	positive regulation of telomere maintenance	31	75	1.625e-02
GO:BP	GO:0071479	cellular response to ionizing radiation	30	72	1.653e-02
GO:BP	GO:0007267	cell-cell signaling	382	1342	1.666e-02
GO:BP	GO:0035113	embryonic appendage morphogenesis	47	126	1.680e-02
GO:BP	GO:0030326	embryonic limb morphogenesis	47	126	1.680e-02
GO:BP	GO:0046777	protein autophosphorylation	63	179	1.680e-02
GO:BP	GO:0060324	face development	24	54	1.680e-02
GO:BP	GO:0044843	cell cycle G1/S phase transition	78	230	1.690e-02
GO:BP	GO:0050982	detection of mechanical stimulus	25	57	1.694e-02
GO:BP	GO:0007004	telomere maintenance via telomerase	26	60	1.695e-02
GO:BP	GO:0044088	regulation of vacuole organization	26	60	1.695e-02
GO:BP	GO:0060997	dendritic spine morphogenesis	26	60	1.695e-02
GO:BP	GO:0086004	regulation of cardiac muscle cell contraction	17	34	1.704e-02
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	50	136	1.728e-02
GO:BP	GO:0046660	female sex differentiation	46	123	1.750e-02
GO:BP	GO:0006119	oxidative phosphorylation	53	146	1.762e-02
GO:BP	GO:0019985	translesion synthesis	14	26	1.780e-02
GO:BP	GO:0018345	protein palmitoylation	14	26	1.780e-02
GO:BP	GO:0010667	negative regulation of cardiac muscle cell apoptotic process	14	26	1.780e-02
GO:BP	GO:0031401	positive regulation of protein modification process	192	637	1.792e-02
GO:BP	GO:0062014	negative regulation of small molecule metabolic process	41	107	1.795e-02
GO:BP	GO:0031647	regulation of protein stability	108	335	1.798e-02
GO:BP	GO:0010770	positive regulation of cell morphogenesis	18	37	1.841e-02
GO:BP	GO:0044770	cell cycle phase transition	163	532	1.852e-02
GO:BP	GO:0050821	protein stabilization	76	224	1.869e-02
GO:BP	GO:0048041	focal adhesion assembly	34	85	1.874e-02
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	48	130	1.891e-02
GO:BP	GO:1902307	positive regulation of sodium ion transmembrane transport	10	16	1.904e-02
GO:BP	GO:0003376	sphingosine-1-phosphate receptor signaling pathway	10	16	1.904e-02
GO:BP	GO:0098974	postsynaptic actin cytoskeleton organization	10	16	1.904e-02
GO:BP	GO:2001057	reactive nitrogen species metabolic process	33	82	1.923e-02
GO:BP	GO:0046328	regulation of JNK cascade	51	140	1.929e-02
GO:BP	GO:0007369	gastrulation	68	197	1.935e-02
GO:BP	GO:1903034	regulation of response to wounding	60	170	1.938e-02
GO:BP	GO:0006670	sphingosine metabolic process	12	21	1.938e-02
GO:BP	GO:0043407	negative regulation of MAP kinase activity	19	40	1.942e-02
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	54	150	1.943e-02
GO:BP	GO:0021915	neural tube development	57	160	1.944e-02
GO:BP	GO:0010565	regulation of ketone metabolic process	47	127	1.964e-02
GO:BP	GO:0043502	regulation of muscle adaptation	32	79	1.964e-02
GO:BP	GO:0051260	protein homooligomerization	70	204	1.976e-02
GO:BP	GO:0033555	multicellular organismal response to stress	38	98	1.994e-02
GO:BP	GO:0046785	microtubule polymerization	38	98	1.994e-02
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	94	287	2.001e-02
GO:BP	GO:0046839	phospholipid dephosphorylation	20	43	2.018e-02
GO:BP	GO:0010664	negative regulation of striated muscle cell apoptotic process	15	29	2.018e-02
GO:BP	GO:0034250	positive regulation of amide metabolic process	15	29	2.018e-02
GO:BP	GO:0042552	myelination	56	157	2.036e-02
GO:BP	GO:0010631	epithelial cell migration	37	95	2.064e-02
GO:BP	GO:0032922	circadian regulation of gene expression	29	70	2.084e-02
GO:BP	GO:0060415	muscle tissue morphogenesis	29	70	2.084e-02
GO:BP	GO:0032414	positive regulation of ion transmembrane transporter activity	29	70	2.084e-02
GO:BP	GO:0045806	negative regulation of endocytosis	28	67	2.119e-02
GO:BP	GO:2000785	regulation of autophagosome assembly	22	49	2.129e-02
GO:BP	GO:0000018	regulation of DNA recombination	52	144	2.129e-02
GO:BP	GO:0003279	cardiac septum development	41	108	2.130e-02
GO:BP	GO:0002011	morphogenesis of an epithelial sheet	27	64	2.139e-02
GO:BP	GO:0051965	positive regulation of synapse assembly	27	64	2.139e-02
GO:BP	GO:0009299	mRNA transcription	23	52	2.151e-02
GO:BP	GO:1903828	negative regulation of protein localization	73	215	2.155e-02
GO:BP	GO:0042158	lipoprotein biosynthetic process	24	55	2.160e-02
GO:BP	GO:0048278	vesicle docking	25	58	2.160e-02
GO:BP	GO:0045778	positive regulation of ossification	24	55	2.160e-02
GO:BP	GO:0007626	locomotory behavior	75	222	2.188e-02
GO:BP	GO:0002221	pattern recognition receptor signaling pathway	88	267	2.191e-02
GO:BP	GO:0035418	protein localization to synapse	35	89	2.191e-02
GO:BP	GO:0008589	regulation of smoothened signaling pathway	35	89	2.191e-02
GO:BP	GO:2000279	negative regulation of DNA biosynthetic process	16	32	2.214e-02
GO:BP	GO:0014850	response to muscle activity	16	32	2.214e-02
GO:BP	GO:0016482	cytosolic transport	51	141	2.215e-02
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	34	86	2.264e-02
GO:BP	GO:0010970	transport along microtubule	62	178	2.274e-02
GO:BP	GO:0046394	carboxylic acid biosynthetic process	103	320	2.288e-02
GO:BP	GO:0098660	inorganic ion transmembrane transport	274	944	2.302e-02
GO:BP	GO:1902993	positive regulation of amyloid precursor protein catabolic process	13	24	2.311e-02
GO:BP	GO:0043405	regulation of MAP kinase activity	43	115	2.316e-02
GO:BP	GO:0046928	regulation of neurotransmitter secretion	33	83	2.331e-02
GO:BP	GO:0036151	phosphatidylcholine acyl-chain remodeling	9	14	2.379e-02
GO:BP	GO:0002087	regulation of respiratory gaseous exchange by nervous system process	9	14	2.379e-02
GO:BP	GO:0046322	negative regulation of fatty acid oxidation	9	14	2.379e-02
GO:BP	GO:0043648	dicarboxylic acid metabolic process	38	99	2.379e-02
GO:BP	GO:0050905	neuromuscular process	61	175	2.386e-02
GO:BP	GO:0055013	cardiac muscle cell development	32	80	2.396e-02
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	42	112	2.414e-02
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	52	145	2.454e-02
GO:BP	GO:0032411	positive regulation of transporter activity	31	77	2.465e-02
GO:BP	GO:0007044	cell-substrate junction assembly	37	96	2.470e-02
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	77	230	2.479e-02
GO:BP	GO:0090201	negative regulation of release of cytochrome c from mitochondria	11	19	2.492e-02
GO:BP	GO:1903830	magnesium ion transmembrane transport	11	19	2.492e-02
GO:BP	GO:0060039	pericardium development	11	19	2.492e-02
GO:BP	GO:0014819	regulation of skeletal muscle contraction	11	19	2.492e-02
GO:BP	GO:0000966	RNA 5’-end processing	18	38	2.506e-02
GO:BP	GO:1901890	positive regulation of cell junction assembly	41	109	2.506e-02
GO:BP	GO:0098698	postsynaptic specialization assembly	18	38	2.506e-02
GO:BP	GO:0021955	central nervous system neuron axonogenesis	18	38	2.506e-02
GO:BP	GO:0042982	amyloid precursor protein metabolic process	30	74	2.509e-02
GO:BP	GO:0061025	membrane fusion	65	189	2.509e-02
GO:BP	GO:0051216	cartilage development	72	213	2.527e-02
GO:BP	GO:0099111	microtubule-based transport	74	220	2.566e-02
GO:BP	GO:0062208	positive regulation of pattern recognition receptor signaling pathway	29	71	2.570e-02
GO:BP	GO:1902414	protein localization to cell junction	44	119	2.600e-02
GO:BP	GO:1902742	apoptotic process involved in development	19	41	2.607e-02
GO:BP	GO:0032511	late endosome to vacuole transport via multivesicular body sorting pathway	14	27	2.620e-02
GO:BP	GO:0018904	ether metabolic process	14	27	2.620e-02
GO:BP	GO:0071480	cellular response to gamma radiation	14	27	2.620e-02
GO:BP	GO:0034504	protein localization to nucleus	102	318	2.620e-02
GO:BP	GO:0032007	negative regulation of TOR signaling	28	68	2.620e-02
GO:BP	GO:0018209	peptidyl-serine modification	64	186	2.632e-02
GO:BP	GO:0008366	axon ensheathment	56	159	2.651e-02
GO:BP	GO:0007272	ensheathment of neurons	56	159	2.651e-02
GO:BP	GO:0035924	cellular response to vascular endothelial growth factor stimulus	27	65	2.660e-02
GO:BP	GO:0006260	DNA replication	92	283	2.667e-02
GO:BP	GO:0044272	sulfur compound biosynthetic process	53	149	2.668e-02
GO:BP	GO:0042058	regulation of epidermal growth factor receptor signaling pathway	26	62	2.698e-02
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	21	47	2.717e-02
GO:BP	GO:0090497	mesenchymal cell migration	25	59	2.728e-02
GO:BP	GO:0001822	kidney development	103	322	2.730e-02
GO:BP	GO:0051650	establishment of vesicle localization	68	200	2.740e-02
GO:BP	GO:0071470	cellular response to osmotic stress	24	56	2.741e-02
GO:BP	GO:0042987	amyloid precursor protein catabolic process	24	56	2.741e-02
GO:BP	GO:0170034	L-amino acid biosynthetic process	23	53	2.745e-02
GO:BP	GO:1900542	regulation of purine nucleotide metabolic process	33	84	2.806e-02
GO:BP	GO:0030516	regulation of axon extension	33	84	2.806e-02
GO:BP	GO:0120034	positive regulation of plasma membrane bounded cell projection assembly	42	113	2.818e-02
GO:BP	GO:0021952	central nervous system projection neuron axonogenesis	15	30	2.886e-02
GO:BP	GO:0001838	embryonic epithelial tube formation	45	123	2.899e-02
GO:BP	GO:0002218	activation of innate immune response	98	305	2.910e-02
GO:BP	GO:2001046	positive regulation of integrin-mediated signaling pathway	8	12	2.931e-02
GO:BP	GO:0106120	positive regulation of sterol biosynthetic process	8	12	2.931e-02
GO:BP	GO:0043508	negative regulation of JUN kinase activity	8	12	2.931e-02
GO:BP	GO:0045542	positive regulation of cholesterol biosynthetic process	8	12	2.931e-02
GO:BP	GO:0034976	response to endoplasmic reticulum stress	88	270	2.950e-02
GO:BP	GO:0140861	DNA repair-dependent chromatin remodeling	12	22	2.990e-02
GO:BP	GO:0048644	muscle organ morphogenesis	31	78	2.990e-02
GO:BP	GO:0016053	organic acid biosynthetic process	103	323	2.990e-02
GO:BP	GO:0045932	negative regulation of muscle contraction	12	22	2.990e-02
GO:BP	GO:0034472	snRNA 3’-end processing	12	22	2.990e-02
GO:BP	GO:0032042	mitochondrial DNA metabolic process	12	22	2.990e-02
GO:BP	GO:0035264	multicellular organism growth	56	160	3.022e-02
GO:BP	GO:0019217	regulation of fatty acid metabolic process	36	94	3.029e-02
GO:BP	GO:0060021	roof of mouth development	36	94	3.029e-02
GO:BP	GO:0031334	positive regulation of protein-containing complex assembly	68	201	3.078e-02
GO:BP	GO:0010644	cell communication by electrical coupling	16	33	3.088e-02
GO:BP	GO:0055088	lipid homeostasis	58	167	3.122e-02
GO:BP	GO:0006405	RNA export from nucleus	35	91	3.154e-02
GO:BP	GO:2000036	regulation of stem cell population maintenance	29	72	3.155e-02
GO:BP	GO:0043549	regulation of kinase activity	133	431	3.173e-02
GO:BP	GO:0042274	ribosomal small subunit biogenesis	39	104	3.198e-02
GO:BP	GO:0044065	regulation of respiratory system process	10	17	3.198e-02
GO:BP	GO:1901018	positive regulation of potassium ion transmembrane transporter activity	10	17	3.198e-02
GO:BP	GO:0002098	tRNA wobble uridine modification	10	17	3.198e-02
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	39	104	3.198e-02
GO:BP	GO:0034614	cellular response to reactive oxygen species	52	147	3.206e-02
GO:BP	GO:0002028	regulation of sodium ion transport	28	69	3.220e-02
GO:BP	GO:1901184	regulation of ERBB signaling pathway	28	69	3.220e-02
GO:BP	GO:0060411	cardiac septum morphogenesis	28	69	3.220e-02
GO:BP	GO:0006779	porphyrin-containing compound biosynthetic process	17	36	3.235e-02
GO:BP	GO:0033014	tetrapyrrole biosynthetic process	17	36	3.235e-02
GO:BP	GO:1902003	regulation of amyloid-beta formation	17	36	3.235e-02
GO:BP	GO:0071345	cellular response to cytokine stimulus	248	854	3.280e-02
GO:BP	GO:0006836	neurotransmitter transport	71	212	3.312e-02
GO:BP	GO:0120033	negative regulation of plasma membrane bounded cell projection assembly	18	39	3.348e-02
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	26	63	3.348e-02
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	51	144	3.348e-02
GO:BP	GO:0008286	insulin receptor signaling pathway	45	124	3.348e-02
GO:BP	GO:0032205	negative regulation of telomere maintenance	18	39	3.348e-02
GO:BP	GO:0090181	regulation of cholesterol metabolic process	18	39	3.348e-02
GO:BP	GO:0046677	response to antibiotic	18	39	3.348e-02
GO:BP	GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway	26	63	3.348e-02
GO:BP	GO:0061053	somite development	33	85	3.356e-02
GO:BP	GO:0006140	regulation of nucleotide metabolic process	33	85	3.356e-02
GO:BP	GO:2000209	regulation of anoikis	13	25	3.402e-02
GO:BP	GO:0099172	presynapse organization	25	60	3.404e-02
GO:BP	GO:0010508	positive regulation of autophagy	56	161	3.418e-02
GO:BP	GO:0043270	positive regulation of monoatomic ion transport	68	202	3.422e-02
GO:BP	GO:0031099	regeneration	68	202	3.422e-02
GO:BP	GO:0090132	epithelium migration	37	98	3.439e-02
GO:BP	GO:0001755	neural crest cell migration	24	57	3.442e-02
GO:BP	GO:0099084	postsynaptic specialization organization	24	57	3.442e-02
GO:BP	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	20	45	3.468e-02
GO:BP	GO:0090148	membrane fission	20	45	3.468e-02
GO:BP	GO:0050771	negative regulation of axonogenesis	23	54	3.470e-02
GO:BP	GO:1904263	positive regulation of TORC1 signaling	23	54	3.470e-02
GO:BP	GO:1904262	negative regulation of TORC1 signaling	21	48	3.478e-02
GO:BP	GO:0034314	Arp2/3 complex-mediated actin nucleation	21	48	3.478e-02
GO:BP	GO:0097106	postsynaptic density organization	21	48	3.478e-02
GO:BP	GO:0006458	‘de novo’ protein folding	21	48	3.478e-02
GO:BP	GO:0019673	GDP-mannose metabolic process	7	10	3.508e-02
GO:BP	GO:0060315	negative regulation of ryanodine-sensitive calcium-release channel activity	7	10	3.508e-02
GO:BP	GO:0097119	postsynaptic density protein 95 clustering	7	10	3.508e-02
GO:BP	GO:2001241	positive regulation of extrinsic apoptotic signaling pathway in absence of ligand	7	10	3.508e-02
GO:BP	GO:0010720	positive regulation of cell development	140	458	3.547e-02
GO:BP	GO:0097120	receptor localization to synapse	31	79	3.568e-02
GO:BP	GO:0001763	morphogenesis of a branching structure	69	206	3.626e-02
GO:BP	GO:0051656	establishment of organelle localization	149	491	3.638e-02
GO:BP	GO:0003002	regionalization	133	433	3.639e-02
GO:BP	GO:1904063	negative regulation of cation transmembrane transport	30	76	3.693e-02
GO:BP	GO:0032273	positive regulation of protein polymerization	35	92	3.711e-02
GO:BP	GO:0039529	RIG-I signaling pathway	14	28	3.725e-02
GO:BP	GO:0009314	response to radiation	134	437	3.753e-02
GO:BP	GO:0001508	action potential	59	172	3.766e-02
GO:BP	GO:0050954	sensory perception of mechanical stimulus	66	196	3.771e-02
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	29	73	3.810e-02
GO:BP	GO:0072093	metanephric renal vesicle formation	4	4	3.850e-02
GO:BP	GO:1900451	positive regulation of glutamate receptor signaling pathway	4	4	3.850e-02
GO:BP	GO:1903278	positive regulation of sodium ion export across plasma membrane	4	4	3.850e-02
GO:BP	GO:0002097	tRNA wobble base modification	11	20	3.850e-02
GO:BP	GO:0042560	pteridine-containing compound catabolic process	4	4	3.850e-02
GO:BP	GO:0009397	folic acid-containing compound catabolic process	4	4	3.850e-02
GO:BP	GO:0048597	post-embryonic camera-type eye morphogenesis	4	4	3.850e-02
GO:BP	GO:1903276	regulation of sodium ion export across plasma membrane	4	4	3.850e-02
GO:BP	GO:0015693	magnesium ion transport	11	20	3.850e-02
GO:BP	GO:1902262	apoptotic process involved in blood vessel morphogenesis	4	4	3.850e-02
GO:BP	GO:0061003	positive regulation of dendritic spine morphogenesis	11	20	3.850e-02
GO:BP	GO:0042273	ribosomal large subunit biogenesis	28	70	3.899e-02
GO:BP	GO:0045669	positive regulation of osteoblast differentiation	28	70	3.899e-02
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	53	152	3.926e-02
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	41	112	3.966e-02
GO:BP	GO:0033209	tumor necrosis factor-mediated signaling pathway	41	112	3.966e-02
GO:BP	GO:0016226	iron-sulfur cluster assembly	15	31	3.966e-02
GO:BP	GO:0031163	metallo-sulfur cluster assembly	15	31	3.966e-02
GO:BP	GO:0048864	stem cell development	33	86	3.983e-02
GO:BP	GO:0043248	proteasome assembly	9	15	4.063e-02
GO:BP	GO:0046520	sphingoid biosynthetic process	9	15	4.063e-02
GO:BP	GO:0014874	response to stimulus involved in regulation of muscle adaptation	9	15	4.063e-02
GO:BP	GO:0046512	sphingosine biosynthetic process	9	15	4.063e-02
GO:BP	GO:0006538	glutamate catabolic process	6	8	4.071e-02
GO:BP	GO:0045650	negative regulation of macrophage differentiation	6	8	4.071e-02
GO:BP	GO:2000586	regulation of platelet-derived growth factor receptor-beta signaling pathway	6	8	4.071e-02
GO:BP	GO:0003344	pericardium morphogenesis	6	8	4.071e-02
GO:BP	GO:1904026	regulation of collagen fibril organization	6	8	4.071e-02
GO:BP	GO:0006785	heme B biosynthetic process	6	8	4.071e-02
GO:BP	GO:0043504	mitochondrial DNA repair	6	8	4.071e-02
GO:BP	GO:0014722	regulation of skeletal muscle contraction by calcium ion signaling	6	8	4.071e-02
GO:BP	GO:0016139	glycoside catabolic process	6	8	4.071e-02
GO:BP	GO:0015959	diadenosine polyphosphate metabolic process	6	8	4.071e-02
GO:BP	GO:0031077	post-embryonic camera-type eye development	6	8	4.071e-02
GO:BP	GO:0046492	heme B metabolic process	6	8	4.071e-02
GO:BP	GO:0043523	regulation of neuron apoptotic process	79	242	4.073e-02
GO:BP	GO:0036294	cellular response to decreased oxygen levels	52	149	4.084e-02
GO:BP	GO:0010628	positive regulation of gene expression	342	1212	4.104e-02
GO:BP	GO:0048709	oligodendrocyte differentiation	40	109	4.104e-02
GO:BP	GO:0042063	gliogenesis	110	352	4.108e-02
GO:BP	GO:1902882	regulation of response to oxidative stress	16	34	4.108e-02
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	16	34	4.108e-02
GO:BP	GO:0040036	regulation of fibroblast growth factor receptor signaling pathway	16	34	4.108e-02
GO:BP	GO:0062125	regulation of mitochondrial gene expression	16	34	4.108e-02
GO:BP	GO:0006536	glutamate metabolic process	16	34	4.108e-02
GO:BP	GO:0030879	mammary gland development	49	139	4.124e-02
GO:BP	GO:0031396	regulation of protein ubiquitination	66	197	4.135e-02
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	36	96	4.135e-02
GO:BP	GO:0043255	regulation of carbohydrate biosynthetic process	36	96	4.135e-02
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	54	156	4.184e-02
GO:BP	GO:0033365	protein localization to organelle	341	1209	4.228e-02
GO:BP	GO:0014032	neural crest cell development	31	80	4.229e-02
GO:BP	GO:0045324	late endosome to vacuole transport	17	37	4.244e-02
GO:BP	GO:0050770	regulation of axonogenesis	51	146	4.270e-02
GO:BP	GO:0010586	miRNA metabolic process	39	106	4.272e-02
GO:BP	GO:0035176	social behavior	23	55	4.292e-02
GO:BP	GO:0014033	neural crest cell differentiation	35	93	4.309e-02
GO:BP	GO:0055092	sterol homeostasis	35	93	4.309e-02
GO:BP	GO:2000781	positive regulation of double-strand break repair	35	93	4.309e-02
GO:BP	GO:0002071	glandular epithelial cell maturation	5	6	4.312e-02
GO:BP	GO:0006111	regulation of gluconeogenesis	21	49	4.312e-02
GO:BP	GO:0003283	atrial septum development	12	23	4.312e-02
GO:BP	GO:1990116	ribosome-associated ubiquitin-dependent protein catabolic process	5	6	4.312e-02
GO:BP	GO:0003415	chondrocyte hypertrophy	5	6	4.312e-02
GO:BP	GO:0000389	mRNA 3’-splice site recognition	5	6	4.312e-02
GO:BP	GO:0051096	positive regulation of helicase activity	5	6	4.312e-02
GO:BP	GO:0010171	body morphogenesis	22	52	4.312e-02
GO:BP	GO:0031999	negative regulation of fatty acid beta-oxidation	5	6	4.312e-02
GO:BP	GO:0021999	neural plate anterior/posterior regionalization	5	6	4.312e-02
GO:BP	GO:0019320	hexose catabolic process	20	46	4.312e-02
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	19	43	4.312e-02
GO:BP	GO:0038084	vascular endothelial growth factor signaling pathway	19	43	4.312e-02
GO:BP	GO:0015961	diadenosine polyphosphate catabolic process	5	6	4.312e-02
GO:BP	GO:0010837	regulation of keratinocyte proliferation	20	46	4.312e-02
GO:BP	GO:0106106	cold-induced thermogenesis	53	153	4.312e-02
GO:BP	GO:0010332	response to gamma radiation	22	52	4.312e-02
GO:BP	GO:0009298	GDP-mannose biosynthetic process	5	6	4.312e-02
GO:BP	GO:0009066	aspartate family amino acid metabolic process	19	43	4.312e-02
GO:BP	GO:1901016	regulation of potassium ion transmembrane transporter activity	18	40	4.312e-02
GO:BP	GO:0031124	mRNA 3’-end processing	20	46	4.312e-02
GO:BP	GO:1901020	negative regulation of calcium ion transmembrane transporter activity	12	23	4.312e-02
GO:BP	GO:0050767	regulation of neurogenesis	117	378	4.312e-02
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	48	136	4.312e-02
GO:BP	GO:0050686	negative regulation of mRNA processing	12	23	4.312e-02
GO:BP	GO:0046929	negative regulation of neurotransmitter secretion	5	6	4.312e-02
GO:BP	GO:0008652	amino acid biosynthetic process	30	77	4.312e-02
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	69	208	4.343e-02
GO:BP	GO:0007029	endoplasmic reticulum organization	38	103	4.385e-02
GO:BP	GO:0072384	organelle transport along microtubule	34	90	4.412e-02
GO:BP	GO:1901264	carbohydrate derivative transport	34	90	4.412e-02
GO:BP	GO:0061077	chaperone-mediated protein folding	29	74	4.449e-02
GO:BP	GO:0045596	negative regulation of cell differentiation	197	671	4.457e-02
GO:BP	GO:0045598	regulation of fat cell differentiation	47	133	4.457e-02
GO:BP	GO:0007265	Ras protein signal transduction	44	123	4.482e-02
GO:BP	GO:0032200	telomere organization	64	191	4.492e-02
GO:BP	GO:0030832	regulation of actin filament length	52	150	4.536e-02
GO:BP	GO:0030324	lung development	66	198	4.536e-02
GO:BP	GO:0051588	regulation of neurotransmitter transport	37	100	4.584e-02
GO:BP	GO:0018105	peptidyl-serine phosphorylation	59	174	4.607e-02
GO:BP	GO:0008360	regulation of cell shape	49	140	4.628e-02
GO:BP	GO:0002262	myeloid cell homeostasis	61	181	4.681e-02
GO:BP	GO:0051282	regulation of sequestering of calcium ion	46	130	4.689e-02
GO:BP	GO:0070129	regulation of mitochondrial translation	13	26	4.696e-02
GO:BP	GO:0060669	embryonic placenta morphogenesis	13	26	4.696e-02
GO:BP	GO:0006515	protein quality control for misfolded or incompletely synthesized proteins	13	26	4.696e-02
GO:BP	GO:0006275	regulation of DNA replication	43	120	4.696e-02
GO:BP	GO:0006007	glucose catabolic process	13	26	4.696e-02
GO:BP	GO:1901607	alpha-amino acid biosynthetic process	27	68	4.733e-02
GO:BP	GO:0060284	regulation of cell development	244	847	4.733e-02
GO:BP	GO:0071396	cellular response to lipid	181	613	4.756e-02
GO:BP	GO:0008064	regulation of actin polymerization or depolymerization	51	147	4.759e-02
GO:BP	GO:0006970	response to osmotic stress	32	84	4.769e-02
GO:BP	GO:0030323	respiratory tube development	67	202	4.799e-02
GO:BP	GO:0006520	amino acid metabolic process	94	297	4.805e-02
GO:BP	GO:0072578	neurotransmitter-gated ion channel clustering	10	18	4.858e-02
GO:BP	GO:0010544	negative regulation of platelet activation	10	18	4.858e-02
GO:BP	GO:0043923	positive regulation by host of viral transcription	10	18	4.858e-02
GO:BP	GO:0061621	canonical glycolysis	10	18	4.858e-02
GO:BP	GO:0061718	glucose catabolic process to pyruvate	10	18	4.858e-02
GO:BP	GO:0016032	viral process	129	423	4.860e-02
GO:BP	GO:0030534	adult behavior	53	154	4.863e-02
GO:BP	GO:0030509	BMP signaling pathway	53	154	4.863e-02
GO:BP	GO:0030510	regulation of BMP signaling pathway	39	107	4.863e-02
GO:BP	GO:0002831	regulation of response to biotic stimulus	161	540	4.918e-02
GO:BP	GO:0051301	cell division	193	658	4.918e-02
GO:BP	GO:0140029	exocytic process	31	81	4.937e-02
GO:BP	GO:0051279	regulation of release of sequestered calcium ion into cytosol	31	81	4.937e-02
GO:BP	GO:0060249	anatomical structure homeostasis	86	269	4.953e-02
GO:BP	GO:0014020	primary neural tube formation	35	94	4.963e-02
GO:BP	GO:0042733	embryonic digit morphogenesis	25	62	4.980e-02
GO:BP	GO:0055023	positive regulation of cardiac muscle tissue growth	14	29	4.988e-02
KEGG	KEGG:01100	Metabolic pathways	516	1537	3.303e-03
KEGG	KEGG:04070	Phosphatidylinositol signaling system	47	97	3.303e-03
KEGG	KEGG:04140	Autophagy - animal	72	165	3.303e-03
KEGG	KEGG:03018	RNA degradation	40	79	3.303e-03
KEGG	KEGG:04260	Cardiac muscle contraction	43	87	3.303e-03
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	65	153	8.789e-03
KEGG	KEGG:00510	N-Glycan biosynthesis	28	53	8.789e-03
KEGG	KEGG:05168	Herpes simplex virus 1 infection	183	506	8.789e-03
KEGG	KEGG:01200	Carbon metabolism	52	115	8.789e-03
KEGG	KEGG:05410	Hypertrophic cardiomyopathy	45	97	8.789e-03
KEGG	KEGG:04360	Axon guidance	74	181	1.167e-02
KEGG	KEGG:05230	Central carbon metabolism in cancer	34	70	1.167e-02
KEGG	KEGG:05414	Dilated cardiomyopathy	46	102	1.167e-02
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	69	168	1.330e-02
KEGG	KEGG:05225	Hepatocellular carcinoma	68	166	1.480e-02
KEGG	KEGG:00562	Inositol phosphate metabolism	34	73	2.436e-02
KEGG	KEGG:01250	Biosynthesis of nucleotide sugars	20	37	2.436e-02
KEGG	KEGG:04010	MAPK signaling pathway	112	301	2.436e-02
KEGG	KEGG:04919	Thyroid hormone signaling pathway	51	121	2.546e-02
KEGG	KEGG:04931	Insulin resistance	46	108	2.998e-02
KEGG	KEGG:00280	Valine, leucine and isoleucine degradation	24	48	2.998e-02
KEGG	KEGG:04340	Hedgehog signaling pathway	27	56	3.004e-02
KEGG	KEGG:04137	Mitophagy - animal	44	103	3.126e-02
KEGG	KEGG:04022	cGMP-PKG signaling pathway	65	164	3.126e-02
KEGG	KEGG:00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	15	26	3.126e-02
KEGG	KEGG:00520	Amino sugar and nucleotide sugar metabolism	24	49	3.430e-02
KEGG	KEGG:05131	Shigellosis	92	246	3.480e-02
KEGG	KEGG:04932	Non-alcoholic fatty liver disease	61	154	3.812e-02
KEGG	KEGG:05213	Endometrial cancer	27	58	4.281e-02
KEGG	KEGG:01524	Platinum drug resistance	32	72	4.407e-02
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	129	363	4.407e-02
KEGG	KEGG:03040	Spliceosome	67	174	4.814e-02
KEGG	KEGG:04714	Thermogenesis	86	232	4.941e-02
KEGG	KEGG:05412	Arrhythmogenic right ventricular cardiomyopathy	36	84	4.941e-02

# write.csv(table_motif2_GOKEGG_genes, "data/new/table_motif2_GOKEGG_genes.csv")

#GO:BP
table_motif2_genes_GOBP <- table_motif2_GOKEGG_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif2_genes_GOBP, "data/table_motif2_genes_GOBP.RDS")

table_motif2_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 2 Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-5.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_motif2_genes_KEGG <- table_motif2_GOKEGG_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif2_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 2 DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-6.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#####Motif 3 DEGs GO KEGG#####
# motif3_genes_matrix <- as.matrix(final_genes_3) 
# colnames(motif3_genes_matrix) <- c("entrezgene_ID")

# saveRDS(motif3_genes_matrix, "data/new/motif3_genes_matrix.RDS")

motif3_genes_matrix <- readRDS("data/new/motif3_genes_matrix.RDS")
length(motif3_genes_matrix)

[1] 231

#231 genes in this set for motif 3

motif3_mat_GOKEGG <- gost(query = motif3_genes_matrix,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif3_GOKEGG_genes <- gostplot(motif3_mat_GOKEGG, capped = FALSE, interactive = TRUE)
motif3_GOKEGG_genes

table_motif3_GOKEGG_genes <- motif3_mat_GOKEGG$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif3_GOKEGG_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0022402	cell cycle process	69	1280	9.207e-31
GO:BP	GO:0007059	chromosome segregation	45	427	9.207e-31
GO:BP	GO:1903047	mitotic cell cycle process	53	745	1.891e-28
GO:BP	GO:0000278	mitotic cell cycle	56	892	1.301e-27
GO:BP	GO:0007049	cell cycle	71	1663	7.400e-26
GO:BP	GO:0010564	regulation of cell cycle process	48	720	1.962e-24
GO:BP	GO:0051276	chromosome organization	42	574	1.225e-22
GO:BP	GO:0140014	mitotic nuclear division	32	282	1.336e-22
GO:BP	GO:0098813	nuclear chromosome segregation	33	323	5.448e-22
GO:BP	GO:0044770	cell cycle phase transition	40	532	5.448e-22
GO:BP	GO:0000070	mitotic sister chromatid segregation	27	193	2.275e-21
GO:BP	GO:0051726	regulation of cell cycle	53	1087	3.696e-21
GO:BP	GO:0006259	DNA metabolic process	51	1005	4.748e-21
GO:BP	GO:0051301	cell division	42	658	1.229e-20
GO:BP	GO:0000819	sister chromatid segregation	28	234	1.908e-20
GO:BP	GO:1901987	regulation of cell cycle phase transition	35	427	1.972e-20
GO:BP	GO:0044772	mitotic cell cycle phase transition	35	428	2.005e-20
GO:BP	GO:0007088	regulation of mitotic nuclear division	22	121	6.255e-20
GO:BP	GO:0000280	nuclear division	35	452	1.086e-19
GO:BP	GO:0000075	cell cycle checkpoint signaling	25	185	1.518e-19
GO:BP	GO:0007346	regulation of mitotic cell cycle	36	492	1.603e-19
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	17	59	5.873e-19
GO:BP	GO:0006281	DNA repair	39	621	5.873e-19
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	22	136	6.884e-19
GO:BP	GO:0051310	metaphase chromosome alignment	20	104	1.149e-18
GO:BP	GO:0007051	spindle organization	25	206	1.735e-18
GO:BP	GO:0006260	DNA replication	28	283	1.979e-18
GO:BP	GO:0048285	organelle fission	35	500	1.979e-18
GO:BP	GO:0051784	negative regulation of nuclear division	17	65	2.984e-18
GO:BP	GO:0010948	negative regulation of cell cycle process	28	289	3.157e-18
GO:BP	GO:0051783	regulation of nuclear division	22	149	4.212e-18
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	26	248	9.826e-18
GO:BP	GO:0051303	establishment of chromosome localization	20	118	1.240e-17
GO:BP	GO:0006261	DNA-templated DNA replication	22	160	1.892e-17
GO:BP	GO:0006974	DNA damage response	44	908	1.941e-17
GO:BP	GO:0045786	negative regulation of cell cycle	30	377	2.973e-17
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	16	62	3.970e-17
GO:BP	GO:0050000	chromosome localization	20	126	4.200e-17
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	15	51	4.914e-17
GO:BP	GO:1905818	regulation of chromosome separation	17	77	4.914e-17
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	15	51	4.914e-17
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	15	51	4.914e-17
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	15	51	4.914e-17
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	18	93	5.349e-17
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	28	327	5.797e-17
GO:BP	GO:0051306	mitotic sister chromatid separation	16	65	7.384e-17
GO:BP	GO:0051985	negative regulation of chromosome segregation	15	53	8.314e-17
GO:BP	GO:1905819	negative regulation of chromosome separation	15	53	8.314e-17
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	15	53	8.314e-17
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	18	96	8.625e-17
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	18	97	1.030e-16
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	24	225	1.128e-16
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	18	100	1.765e-16
GO:BP	GO:0051304	chromosome separation	17	84	1.873e-16
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	15	57	2.529e-16
GO:BP	GO:0033045	regulation of sister chromatid segregation	18	107	5.966e-16
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	14	49	8.637e-16
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	14	49	8.637e-16
GO:BP	GO:0071173	spindle assembly checkpoint signaling	14	49	8.637e-16
GO:BP	GO:0031577	spindle checkpoint signaling	14	50	1.170e-15
GO:BP	GO:0051983	regulation of chromosome segregation	19	132	1.385e-15
GO:BP	GO:0007052	mitotic spindle organization	19	134	1.822e-15
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	14	54	3.730e-15
GO:BP	GO:0000226	microtubule cytoskeleton organization	35	670	8.784e-15
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	20	169	9.339e-15
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	20	172	1.303e-14
GO:BP	GO:0033044	regulation of chromosome organization	22	242	7.483e-14
GO:BP	GO:0090068	positive regulation of cell cycle process	22	262	3.879e-13
GO:BP	GO:0006996	organelle organization	80	3594	5.571e-13
GO:BP	GO:2001251	negative regulation of chromosome organization	15	97	1.000e-12
GO:BP	GO:0033043	regulation of organelle organization	42	1148	1.438e-12
GO:BP	GO:0007017	microtubule-based process	39	999	1.774e-12
GO:BP	GO:0045787	positive regulation of cell cycle	24	351	1.983e-12
GO:BP	GO:0051225	spindle assembly	16	136	1.028e-11
GO:BP	GO:0033554	cellular response to stress	52	1830	1.603e-11
GO:BP	GO:0051052	regulation of DNA metabolic process	26	500	8.905e-11
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	11	63	7.329e-10
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	8	23	1.044e-09
GO:BP	GO:0044839	cell cycle G2/M phase transition	15	156	1.057e-09
GO:BP	GO:0006302	double-strand break repair	20	319	1.275e-09
GO:BP	GO:1903083	protein localization to condensed chromosome	7	15	1.504e-09
GO:BP	GO:0034501	protein localization to kinetochore	7	15	1.504e-09
GO:BP	GO:0051656	establishment of organelle localization	24	491	2.209e-09
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	14	139	2.494e-09
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	12	93	3.174e-09
GO:BP	GO:0007010	cytoskeleton organization	43	1529	3.474e-09
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	9	41	5.251e-09
GO:BP	GO:0006310	DNA recombination	20	347	5.251e-09
GO:BP	GO:0034502	protein localization to chromosome	13	126	8.517e-09
GO:BP	GO:0000725	recombinational repair	15	193	1.905e-08
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	12	114	3.302e-08
GO:BP	GO:0140694	membraneless organelle assembly	21	430	3.471e-08
GO:BP	GO:0051640	organelle localization	25	620	4.270e-08
GO:BP	GO:0010639	negative regulation of organelle organization	19	352	4.305e-08
GO:BP	GO:0031570	DNA integrity checkpoint signaling	12	123	7.646e-08
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	12	124	8.308e-08
GO:BP	GO:0051716	cellular response to stimulus	111	7376	8.331e-08
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	8	40	1.135e-07
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	11	105	1.630e-07
GO:BP	GO:0006338	chromatin remodeling	26	725	2.081e-07
GO:BP	GO:0034508	centromere complex assembly	7	29	2.646e-07
GO:BP	GO:0051053	negative regulation of DNA metabolic process	12	139	2.890e-07
GO:BP	GO:0051338	regulation of transferase activity	21	498	4.133e-07
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	11	118	5.351e-07
GO:BP	GO:0006275	regulation of DNA replication	11	120	6.324e-07
GO:BP	GO:0032465	regulation of cytokinesis	10	94	6.652e-07
GO:BP	GO:0032467	positive regulation of cytokinesis	8	50	6.692e-07
GO:BP	GO:0048522	positive regulation of cellular process	93	5920	6.943e-07
GO:BP	GO:0006325	chromatin organization	28	884	6.943e-07
GO:BP	GO:0000724	double-strand break repair via homologous recombination	13	188	9.290e-07
GO:BP	GO:0071824	protein-DNA complex organization	15	262	9.911e-07
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	9	74	9.931e-07
GO:BP	GO:0065004	protein-DNA complex assembly	14	241	2.362e-06
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	8	59	2.411e-06
GO:BP	GO:0006950	response to stress	69	3948	2.540e-06
GO:BP	GO:0007098	centrosome cycle	11	140	2.834e-06
GO:BP	GO:0050896	response to stimulus	122	8999	4.140e-06
GO:BP	GO:0016043	cellular component organization	114	8184	4.262e-06
GO:BP	GO:0060236	regulation of mitotic spindle organization	7	44	4.888e-06
GO:BP	GO:0048518	positive regulation of biological process	94	6264	5.314e-06
GO:BP	GO:0044786	cell cycle DNA replication	7	45	5.647e-06
GO:BP	GO:0051128	regulation of cellular component organization	49	2433	6.119e-06
GO:BP	GO:0050790	regulation of catalytic activity	27	928	6.206e-06
GO:BP	GO:0031023	microtubule organizing center organization	11	153	6.551e-06
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	8	70	8.561e-06
GO:BP	GO:0051984	positive regulation of chromosome segregation	6	30	8.563e-06
GO:BP	GO:0090224	regulation of spindle organization	7	48	8.563e-06
GO:BP	GO:1905820	positive regulation of chromosome separation	6	32	1.257e-05
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	11	164	1.257e-05
GO:BP	GO:0045814	negative regulation of gene expression, epigenetic	12	200	1.257e-05
GO:BP	GO:1905832	positive regulation of spindle assembly	4	8	1.328e-05
GO:BP	GO:0071840	cellular component organization or biogenesis	114	8393	1.734e-05
GO:BP	GO:0051129	negative regulation of cellular component organization	22	701	2.392e-05
GO:BP	GO:0048523	negative regulation of cellular process	85	5629	2.421e-05
GO:BP	GO:0010212	response to ionizing radiation	10	141	2.423e-05
GO:BP	GO:0009314	response to radiation	17	437	2.455e-05
GO:BP	GO:0051321	meiotic cell cycle	14	297	2.455e-05
GO:BP	GO:0006270	DNA replication initiation	6	37	2.919e-05
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	5	21	3.089e-05
GO:BP	GO:0000077	DNA damage checkpoint signaling	9	114	3.359e-05
GO:BP	GO:0043085	positive regulation of catalytic activity	19	554	3.565e-05
GO:BP	GO:0032886	regulation of microtubule-based process	13	266	3.896e-05
GO:BP	GO:0051302	regulation of cell division	11	188	4.400e-05
GO:BP	GO:0033260	nuclear DNA replication	6	41	5.242e-05
GO:BP	GO:0070925	organelle assembly	27	1046	5.275e-05
GO:BP	GO:0048519	negative regulation of biological process	86	5834	5.297e-05
GO:BP	GO:0035556	intracellular signal transduction	53	2965	5.841e-05
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	5	24	5.841e-05
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	5	24	5.841e-05
GO:BP	GO:0007143	female meiotic nuclear division	6	42	5.841e-05
GO:BP	GO:0090231	regulation of spindle checkpoint	5	25	7.150e-05
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	5	25	7.150e-05
GO:BP	GO:0140013	meiotic nuclear division	11	202	8.245e-05
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	7	69	8.699e-05
GO:BP	GO:0051781	positive regulation of cell division	8	98	9.171e-05
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	7	71	1.042e-04
GO:BP	GO:1903490	positive regulation of mitotic cytokinesis	4	13	1.091e-04
GO:BP	GO:0051347	positive regulation of transferase activity	13	296	1.130e-04
GO:BP	GO:1901976	regulation of cell cycle checkpoint	6	48	1.226e-04
GO:BP	GO:0040029	epigenetic regulation of gene expression	13	299	1.244e-04
GO:BP	GO:0042770	signal transduction in response to DNA damage	10	173	1.285e-04
GO:BP	GO:0045859	regulation of protein kinase activity	15	402	1.508e-04
GO:BP	GO:0090307	mitotic spindle assembly	7	76	1.575e-04
GO:BP	GO:0031297	replication fork processing	6	51	1.704e-04
GO:BP	GO:0006271	DNA strand elongation involved in DNA replication	4	15	1.924e-04
GO:BP	GO:0000018	regulation of DNA recombination	9	144	1.924e-04
GO:BP	GO:0044771	meiotic cell cycle phase transition	4	15	1.924e-04
GO:BP	GO:0071478	cellular response to radiation	10	182	1.924e-04
GO:BP	GO:1903046	meiotic cell cycle process	11	224	1.996e-04
GO:BP	GO:1902412	regulation of mitotic cytokinesis	4	16	2.507e-04
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	6	55	2.548e-04
GO:BP	GO:0031507	heterochromatin formation	9	151	2.751e-04
GO:BP	GO:0000910	cytokinesis	10	192	2.961e-04
GO:BP	GO:0050789	regulation of biological process	146	12336	2.961e-04
GO:BP	GO:0090169	regulation of spindle assembly	5	34	3.034e-04
GO:BP	GO:0043549	regulation of kinase activity	15	431	3.158e-04
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	11	242	3.918e-04
GO:BP	GO:0006301	postreplication repair	5	36	3.979e-04
GO:BP	GO:0050794	regulation of cellular process	142	11946	4.151e-04
GO:BP	GO:0051054	positive regulation of DNA metabolic process	12	291	4.276e-04
GO:BP	GO:0019953	sexual reproduction	26	1122	4.382e-04
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	5	37	4.417e-04
GO:BP	GO:0009966	regulation of signal transduction	51	3034	4.417e-04
GO:BP	GO:0022616	DNA strand elongation	5	37	4.417e-04
GO:BP	GO:0051649	establishment of localization in cell	38	2010	5.228e-04
GO:BP	GO:0000076	DNA replication checkpoint signaling	4	20	5.889e-04
GO:BP	GO:1904666	regulation of ubiquitin protein ligase activity	4	20	5.889e-04
GO:BP	GO:0045132	meiotic chromosome segregation	7	96	6.342e-04
GO:BP	GO:0044093	positive regulation of molecular function	22	884	6.504e-04
GO:BP	GO:0071897	DNA biosynthetic process	9	172	6.981e-04
GO:BP	GO:0051383	kinetochore organization	4	21	7.069e-04
GO:BP	GO:0007099	centriole replication	5	43	8.925e-04
GO:BP	GO:0031109	microtubule polymerization or depolymerization	8	138	8.984e-04
GO:BP	GO:0000731	DNA synthesis involved in DNA repair	5	44	9.889e-04
GO:BP	GO:0046599	regulation of centriole replication	4	23	1.009e-03
GO:BP	GO:0071479	cellular response to ionizing radiation	6	72	1.048e-03
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	5	45	1.087e-03
GO:BP	GO:1900264	positive regulation of DNA-directed DNA polymerase activity	3	9	1.106e-03
GO:BP	GO:0046601	positive regulation of centriole replication	3	9	1.106e-03
GO:BP	GO:0051298	centrosome duplication	6	74	1.199e-03
GO:BP	GO:0010638	positive regulation of organelle organization	15	492	1.252e-03
GO:BP	GO:0010824	regulation of centrosome duplication	5	47	1.311e-03
GO:BP	GO:0065007	biological regulation	147	12743	1.313e-03
GO:BP	GO:0065009	regulation of molecular function	30	1496	1.313e-03
GO:BP	GO:0140273	repair of mitotic kinetochore microtubule attachment defect	2	2	1.402e-03
GO:BP	GO:0140274	repair of kinetochore microtubule attachment defect	2	2	1.402e-03
GO:BP	GO:0099607	lateral attachment of mitotic spindle microtubules to kinetochore	2	2	1.402e-03
GO:BP	GO:0098534	centriole assembly	5	48	1.410e-03
GO:BP	GO:0009628	response to abiotic stimulus	25	1144	1.413e-03
GO:BP	GO:1904668	positive regulation of ubiquitin protein ligase activity	3	10	1.466e-03
GO:BP	GO:0031055	chromatin remodeling at centromere	3	10	1.466e-03
GO:BP	GO:2000104	negative regulation of DNA-templated DNA replication	3	10	1.466e-03
GO:BP	GO:0034080	CENP-A containing chromatin assembly	3	10	1.466e-03
GO:BP	GO:0008156	negative regulation of DNA replication	4	26	1.518e-03
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	6	80	1.725e-03
GO:BP	GO:0045910	negative regulation of DNA recombination	5	51	1.820e-03
GO:BP	GO:0022414	reproductive process	31	1608	1.902e-03
GO:BP	GO:0051641	cellular localization	56	3661	1.905e-03
GO:BP	GO:0051987	positive regulation of attachment of spindle microtubules to kinetochore	3	11	1.938e-03
GO:BP	GO:0051256	mitotic spindle midzone assembly	3	11	1.938e-03
GO:BP	GO:0051493	regulation of cytoskeleton organization	15	517	1.967e-03
GO:BP	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	4	28	1.975e-03
GO:BP	GO:0046605	regulation of centrosome cycle	5	54	2.320e-03
GO:BP	GO:0007056	spindle assembly involved in female meiosis	3	12	2.498e-03
GO:BP	GO:0000022	mitotic spindle elongation	3	12	2.498e-03
GO:BP	GO:0090267	positive regulation of mitotic cell cycle spindle assembly checkpoint	3	12	2.498e-03
GO:BP	GO:1902751	positive regulation of cell cycle G2/M phase transition	4	31	2.903e-03
GO:BP	GO:0048583	regulation of response to stimulus	59	3993	2.942e-03
GO:BP	GO:0090232	positive regulation of spindle checkpoint	3	13	3.154e-03
GO:BP	GO:0006264	mitochondrial DNA replication	3	13	3.154e-03
GO:BP	GO:0007144	female meiosis I	3	13	3.154e-03
GO:BP	GO:0023051	regulation of signaling	53	3478	3.206e-03
GO:BP	GO:0080090	regulation of primary metabolic process	74	5390	3.323e-03
GO:BP	GO:0010646	regulation of cell communication	53	3486	3.355e-03
GO:BP	GO:0043009	chordate embryonic development	17	671	3.355e-03
GO:BP	GO:0007292	female gamete generation	8	174	3.666e-03
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	5	61	3.810e-03
GO:BP	GO:0046385	deoxyribose phosphate biosynthetic process	3	14	3.810e-03
GO:BP	GO:0009265	2’-deoxyribonucleotide biosynthetic process	3	14	3.810e-03
GO:BP	GO:0009263	deoxyribonucleotide biosynthetic process	3	14	3.810e-03
GO:BP	GO:0051231	spindle elongation	3	14	3.810e-03
GO:BP	GO:0051255	spindle midzone assembly	3	14	3.810e-03
GO:BP	GO:0000281	mitotic cytokinesis	6	95	3.924e-03
GO:BP	GO:0006282	regulation of DNA repair	9	225	4.170e-03
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	17	692	4.586e-03
GO:BP	GO:0090306	meiotic spindle assembly	3	15	4.628e-03
GO:BP	GO:0030174	regulation of DNA-templated DNA replication initiation	3	15	4.628e-03
GO:BP	GO:0034728	nucleosome organization	7	138	4.674e-03
GO:BP	GO:1902115	regulation of organelle assembly	9	234	5.404e-03
GO:BP	GO:0071214	cellular response to abiotic stimulus	11	339	5.404e-03
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	8	186	5.404e-03
GO:BP	GO:0104004	cellular response to environmental stimulus	11	339	5.404e-03
GO:BP	GO:0031399	regulation of protein modification process	22	1049	5.546e-03
GO:BP	GO:0007276	gamete generation	19	841	5.635e-03
GO:BP	GO:2000779	regulation of double-strand break repair	7	143	5.635e-03
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	4	38	5.733e-03
GO:BP	GO:2000780	negative regulation of double-strand break repair	4	39	6.316e-03
GO:BP	GO:0009987	cellular process	200	20247	6.334e-03
GO:BP	GO:0006997	nucleus organization	7	147	6.417e-03
GO:BP	GO:0071932	replication fork reversal	2	4	6.417e-03
GO:BP	GO:0070571	negative regulation of neuron projection regeneration	3	17	6.417e-03
GO:BP	GO:0031508	pericentric heterochromatin formation	2	4	6.417e-03
GO:BP	GO:0007089	traversing start control point of mitotic cell cycle	2	4	6.417e-03
GO:BP	GO:0007057	spindle assembly involved in female meiosis I	2	4	6.417e-03
GO:BP	GO:0031573	mitotic intra-S DNA damage checkpoint signaling	3	17	6.417e-03
GO:BP	GO:0045842	positive regulation of mitotic metaphase/anaphase transition	3	17	6.417e-03
GO:BP	GO:0051382	kinetochore assembly	3	17	6.417e-03
GO:BP	GO:2000298	regulation of Rho-dependent protein serine/threonine kinase activity	2	4	6.417e-03
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	5	70	6.509e-03
GO:BP	GO:0045738	negative regulation of DNA repair	4	41	7.293e-03
GO:BP	GO:1902101	positive regulation of metaphase/anaphase transition of cell cycle	3	18	7.407e-03
GO:BP	GO:0036297	interstrand cross-link repair	4	42	7.943e-03
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	8	202	8.541e-03
GO:BP	GO:1901978	positive regulation of cell cycle checkpoint	3	19	8.639e-03
GO:BP	GO:0106030	neuron projection fasciculation	3	20	1.002e-02
GO:BP	GO:0007413	axonal fasciculation	3	20	1.002e-02
GO:BP	GO:1902292	cell cycle DNA replication initiation	2	5	1.007e-02
GO:BP	GO:1902315	nuclear cell cycle DNA replication initiation	2	5	1.007e-02
GO:BP	GO:0043137	DNA replication, removal of RNA primer	2	5	1.007e-02
GO:BP	GO:1905784	regulation of anaphase-promoting complex-dependent catabolic process	2	5	1.007e-02
GO:BP	GO:0007165	signal transduction	78	6002	1.007e-02
GO:BP	GO:1902975	mitotic DNA replication initiation	2	5	1.007e-02
GO:BP	GO:0006297	nucleotide-excision repair, DNA gap filling	2	5	1.007e-02
GO:BP	GO:0006334	nucleosome assembly	6	118	1.063e-02
GO:BP	GO:0006284	base-excision repair	4	46	1.073e-02
GO:BP	GO:0051443	positive regulation of ubiquitin-protein transferase activity	3	21	1.120e-02
GO:BP	GO:0051294	establishment of spindle orientation	4	47	1.156e-02
GO:BP	GO:0032042	mitochondrial DNA metabolic process	3	22	1.275e-02
GO:BP	GO:0000212	meiotic spindle organization	3	22	1.275e-02
GO:BP	GO:0019222	regulation of metabolic process	88	7035	1.302e-02
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	5	83	1.307e-02
GO:BP	GO:0033365	protein localization to organelle	23	1209	1.334e-02
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	6	124	1.334e-02
GO:BP	GO:0048585	negative regulation of response to stimulus	29	1680	1.399e-02
GO:BP	GO:0090402	oncogene-induced cell senescence	2	6	1.420e-02
GO:BP	GO:0016321	female meiosis chromosome segregation	2	6	1.420e-02
GO:BP	GO:0071139	resolution of DNA recombination intermediates	2	6	1.420e-02
GO:BP	GO:0045162	clustering of voltage-gated sodium channels	2	6	1.420e-02
GO:BP	GO:0032506	cytokinetic process	4	50	1.420e-02
GO:BP	GO:0080135	regulation of cellular response to stress	13	519	1.566e-02
GO:BP	GO:0060255	regulation of macromolecule metabolic process	82	6492	1.583e-02
GO:BP	GO:1902117	positive regulation of organelle assembly	5	89	1.719e-02
GO:BP	GO:0044843	cell cycle G1/S phase transition	8	230	1.767e-02
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	3	25	1.772e-02
GO:BP	GO:0009893	positive regulation of metabolic process	51	3597	1.775e-02
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	2	7	1.905e-02
GO:BP	GO:0032954	regulation of cytokinetic process	2	7	1.905e-02
GO:BP	GO:0044785	metaphase/anaphase transition of meiotic cell cycle	2	7	1.905e-02
GO:BP	GO:1903436	regulation of mitotic cytokinetic process	2	7	1.905e-02
GO:BP	GO:1903438	positive regulation of mitotic cytokinetic process	2	7	1.905e-02
GO:BP	GO:0007154	cell communication	82	6540	1.932e-02
GO:BP	GO:0019985	translesion synthesis	3	26	1.938e-02
GO:BP	GO:0035295	tube development	21	1101	1.981e-02
GO:BP	GO:0008406	gonad development	8	238	2.104e-02
GO:BP	GO:0097190	apoptotic signaling pathway	14	606	2.104e-02
GO:BP	GO:0007548	sex differentiation	9	294	2.125e-02
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	8	239	2.146e-02
GO:BP	GO:0007062	sister chromatid cohesion	4	57	2.146e-02
GO:BP	GO:0031102	neuron projection regeneration	4	58	2.281e-02
GO:BP	GO:0061982	meiosis I cell cycle process	6	141	2.345e-02
GO:BP	GO:0045137	development of primary sexual characteristics	8	243	2.349e-02
GO:BP	GO:1901873	regulation of post-translational protein modification	8	244	2.402e-02
GO:BP	GO:2001033	negative regulation of double-strand break repair via nonhomologous end joining	2	8	2.408e-02
GO:BP	GO:0097681	double-strand break repair via alternative nonhomologous end joining	2	8	2.408e-02
GO:BP	GO:1902425	positive regulation of attachment of mitotic spindle microtubules to kinetochore	2	8	2.408e-02
GO:BP	GO:0046785	microtubule polymerization	5	98	2.433e-02
GO:BP	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	3	29	2.545e-02
GO:BP	GO:0023052	signaling	81	6515	2.585e-02
GO:BP	GO:0000002	mitochondrial genome maintenance	3	30	2.785e-02
GO:BP	GO:0031396	regulation of protein ubiquitination	7	197	2.785e-02
GO:BP	GO:0000912	assembly of actomyosin apparatus involved in cytokinesis	2	9	2.950e-02
GO:BP	GO:1904776	regulation of protein localization to cell cortex	2	9	2.950e-02
GO:BP	GO:0051293	establishment of spindle localization	4	63	2.950e-02
GO:BP	GO:0000915	actomyosin contractile ring assembly	2	9	2.950e-02
GO:BP	GO:0062033	positive regulation of mitotic sister chromatid segregation	2	9	2.950e-02
GO:BP	GO:1902423	regulation of attachment of mitotic spindle microtubules to kinetochore	2	9	2.950e-02
GO:BP	GO:0032201	telomere maintenance via semi-conservative replication	2	9	2.950e-02
GO:BP	GO:0046602	regulation of mitotic centrosome separation	2	9	2.950e-02
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	9	312	2.950e-02
GO:BP	GO:0006468	protein phosphorylation	22	1227	3.045e-02
GO:BP	GO:0048609	multicellular organismal reproductive process	19	1000	3.106e-02
GO:BP	GO:2001252	positive regulation of chromosome organization	5	105	3.127e-02
GO:BP	GO:0006298	mismatch repair	3	32	3.216e-02
GO:BP	GO:0070570	regulation of neuron projection regeneration	3	32	3.216e-02
GO:BP	GO:0048856	anatomical structure development	75	5997	3.377e-02
GO:BP	GO:0016310	phosphorylation	23	1320	3.440e-02
GO:BP	GO:0009411	response to UV	6	155	3.456e-02
GO:BP	GO:1901031	regulation of response to reactive oxygen species	2	10	3.559e-02
GO:BP	GO:0044837	actomyosin contractile ring organization	2	10	3.559e-02
GO:BP	GO:0009968	negative regulation of signal transduction	23	1326	3.594e-02
GO:BP	GO:0051653	spindle localization	4	68	3.686e-02
GO:BP	GO:0051445	regulation of meiotic cell cycle	4	68	3.686e-02
GO:BP	GO:0030010	establishment of cell polarity	6	159	3.847e-02
GO:BP	GO:0035239	tube morphogenesis	17	879	4.091e-02
GO:BP	GO:0035090	maintenance of apical/basal cell polarity	2	11	4.191e-02
GO:BP	GO:0033504	floor plate development	2	11	4.191e-02
GO:BP	GO:0033314	mitotic DNA replication checkpoint signaling	2	11	4.191e-02
GO:BP	GO:0045199	maintenance of epithelial cell apical/basal polarity	2	11	4.191e-02
GO:BP	GO:0072711	cellular response to hydroxyurea	2	11	4.191e-02
GO:BP	GO:0072697	protein localization to cell cortex	2	11	4.191e-02
GO:BP	GO:0006915	apoptotic process	30	1923	4.273e-02
GO:BP	GO:0032502	developmental process	80	6553	4.317e-02
GO:BP	GO:0072331	signal transduction by p53 class mediator	6	164	4.347e-02
GO:BP	GO:0060562	epithelial tube morphogenesis	9	336	4.443e-02
GO:BP	GO:0023057	negative regulation of signaling	24	1435	4.457e-02
GO:BP	GO:0010648	negative regulation of cell communication	24	1436	4.483e-02
GO:BP	GO:0007275	multicellular organism development	61	4727	4.510e-02
GO:BP	GO:0000132	establishment of mitotic spindle orientation	3	37	4.549e-02
GO:BP	GO:0051246	regulation of protein metabolic process	29	1855	4.705e-02
GO:BP	GO:0000727	double-strand break repair via break-induced replication	2	12	4.798e-02
GO:BP	GO:0072710	response to hydroxyurea	2	12	4.798e-02
GO:BP	GO:0046549	retinal cone cell development	2	12	4.798e-02
GO:BP	GO:0045161	neuronal ion channel clustering	2	12	4.798e-02
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	2	12	4.798e-02
GO:BP	GO:0042276	error-prone translesion synthesis	2	12	4.798e-02
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	3	38	4.801e-02
KEGG	KEGG:04110	Cell cycle	18	157	1.045e-11
KEGG	KEGG:03030	DNA replication	10	36	2.743e-10
KEGG	KEGG:03430	Mismatch repair	5	23	2.299e-04
KEGG	KEGG:04115	p53 signaling pathway	7	74	6.435e-04
KEGG	KEGG:03440	Homologous recombination	5	41	2.625e-03
KEGG	KEGG:03410	Base excision repair	5	44	3.088e-03
KEGG	KEGG:03460	Fanconi anemia pathway	5	54	7.063e-03
KEGG	KEGG:03420	Nucleotide excision repair	5	61	1.094e-02

# write.csv(table_motif3_GOKEGG_genes, "data/new/table_motif3_GOKEGG_genes.csv")

#GO:BP
table_motif3_genes_GOBP <- table_motif3_GOKEGG_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif3_genes_GOBP, "data/table_motif3_genes_GOBP.RDS")

table_motif3_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 3 Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-8.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_motif3_genes_KEGG <- table_motif3_GOKEGG_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif3_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Motif 3 DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif GO KEGG Final Genes-9.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

###Look at Unassigned Gene Set Cormotif

#now let's pull out the genes that were not assigned to a motif from above

#this one is giving me an issue with wflow_build so I'll fix it later

unassigned_genes_list <- readRDS("data/new/Cormotif/unassigned_genes_Cormotif.RDS")

#with these unassigned genes, I want to plot logFC and GO/KEGG of unassigned genes
#####logFC#####

##no motif genes
unassign_genes_fin <- unassigned_genes_list
length(unassign_genes_fin)

[1] 2232

#2232 genes 

#Combine the toptables I have from pairwise analysis into a single dataframe
combined_toptables_dxr <- bind_rows(
  d24_toptable_dxr,
  d24r_toptable_dxr,
  d144r_toptable_dxr)

#Filter the data based on each motif
# filt_toptable_dxr_fin_unassign <- as.data.frame(combined_toptables_dxr) %>% 
#   dplyr::filter(Entrez_ID  %in% unassign_genes_fin) %>% 
#   mutate(absFC = abs(logFC)) %>% 
#   mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
#   ggplot(., aes(x = time, y = logFC))+
#   geom_boxplot(aes(fill = time))+
#   scale_fill_manual(values = time_col)+
#   guides(fill = guide_legend(title = "Time"))+
#   theme_bw()+
#   xlab(" ")+
#   ylab("logFC")+
#   theme_bw()+
#   ggtitle("LogFC of Unassigned Genes (n=2232)")+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         strip.background = element_rect(fill = "#CAD899"),
#         axis.text.x = element_text(size = 8, colour = "white", angle = 15),
#         strip.text.x = element_text(size = 12, colour = "black", face = "bold"))
# 
# filt_toptable_dxr_fin_unassign


# filt_toptable_abs_fin_unassign <- as.data.frame(combined_toptables_dxr) %>% 
#   dplyr::filter(Entrez_ID  %in% unassign_genes_fin) %>% 
#   mutate(absFC = abs(logFC)) %>% 
#   mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
#   ggplot(., aes(x = time, y = absFC))+
#   geom_boxplot(aes(fill = time))+
#   scale_fill_manual(values = time_col)+
#   guides(fill = guide_legend(title = "Time"))+
#   theme_bw()+
#   xlab(" ")+
#   ylab("|logFC|")+
#   theme_bw()+
#   ggtitle("Abs LogFC of Unassigned Genes (n=2232)")+
#   theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
#         axis.title = element_text(size = 15, colour = "black"),
#         strip.background = element_rect(fill = "#CAD899"),
#         axis.text.x = element_text(size = 8, colour = "white", angle = 15),
#         strip.text.x = element_text(size = 12, colour = "black", face = "bold"))
# 
# filt_toptable_abs_fin_unassign

####GO KEGG####
unassigned_genes_matrix <- as.matrix(unassigned_genes_list)
length(unassigned_genes_matrix)

[1] 2232

#2232 genes in this set

unassign_mat_GOKEGG <- gost(query = unassigned_genes_matrix,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

unassign_GOKEGG_genes <- gostplot(unassign_mat_GOKEGG, capped = FALSE, interactive = TRUE)
unassign_GOKEGG_genes

table_unassign_GOKEGG_genes <- unassign_mat_GOKEGG$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_unassign_GOKEGG_genes %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0022402	cell cycle process	273	1280	3.208e-39
GO:BP	GO:0007049	cell cycle	320	1663	2.070e-37
GO:BP	GO:0000278	mitotic cell cycle	205	892	1.338e-33
GO:BP	GO:0006996	organelle organization	537	3594	4.972e-33
GO:BP	GO:1903047	mitotic cell cycle process	179	745	9.607e-32
GO:BP	GO:0051301	cell division	156	658	1.128e-26
GO:BP	GO:0033554	cellular response to stress	304	1830	8.255e-24
GO:BP	GO:0007059	chromosome segregation	110	427	2.368e-21
GO:BP	GO:0051726	regulation of cell cycle	202	1087	1.158e-20
GO:BP	GO:0010564	regulation of cell cycle process	149	720	3.253e-19
GO:BP	GO:0048285	organelle fission	117	500	3.529e-19
GO:BP	GO:0000280	nuclear division	109	452	7.327e-19
GO:BP	GO:0044770	cell cycle phase transition	120	532	2.257e-18
GO:BP	GO:0065007	biological regulation	1348	12743	3.593e-18
GO:BP	GO:0048522	positive regulation of cellular process	712	5920	9.277e-17
GO:BP	GO:0098813	nuclear chromosome segregation	84	323	1.799e-16
GO:BP	GO:0050789	regulation of biological process	1304	12336	1.799e-16
GO:BP	GO:0035556	intracellular signal transduction	406	2965	2.038e-16
GO:BP	GO:0140014	mitotic nuclear division	77	282	2.306e-16
GO:BP	GO:0080090	regulation of primary metabolic process	656	5390	3.227e-16
GO:BP	GO:0051276	chromosome organization	121	574	3.227e-16
GO:BP	GO:0006974	DNA damage response	166	908	3.356e-16
GO:BP	GO:0000070	mitotic sister chromatid segregation	61	193	3.798e-16
GO:BP	GO:0044772	mitotic cell cycle phase transition	99	428	6.365e-16
GO:BP	GO:0051641	cellular localization	477	3661	7.907e-16
GO:BP	GO:0050794	regulation of cellular process	1265	11946	1.032e-15
GO:BP	GO:0000819	sister chromatid segregation	67	234	2.195e-15
GO:BP	GO:0048518	positive regulation of biological process	735	6264	6.012e-15
GO:BP	GO:1901987	regulation of cell cycle phase transition	94	427	1.162e-13
GO:BP	GO:0032502	developmental process	754	6553	2.467e-13
GO:BP	GO:0007346	regulation of mitotic cell cycle	102	492	4.199e-13
GO:BP	GO:0006260	DNA replication	70	283	1.454e-12
GO:BP	GO:0019538	protein metabolic process	568	4721	2.242e-12
GO:BP	GO:0006259	DNA metabolic process	166	1005	3.752e-12
GO:BP	GO:0070925	organelle assembly	168	1046	3.029e-11
GO:BP	GO:0036211	protein modification process	369	2846	3.029e-11
GO:BP	GO:0023051	regulation of signaling	435	3478	3.149e-11
GO:BP	GO:0006261	DNA-templated DNA replication	47	160	4.629e-11
GO:BP	GO:0070727	cellular macromolecule localization	361	2782	4.991e-11
GO:BP	GO:0051179	localization	642	5555	6.201e-11
GO:BP	GO:0010646	regulation of cell communication	434	3486	6.383e-11
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	73	327	7.886e-11
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	485	3990	8.037e-11
GO:BP	GO:0007275	multicellular organism development	559	4727	8.630e-11
GO:BP	GO:0008104	protein localization	358	2770	9.831e-11
GO:BP	GO:0051649	establishment of localization in cell	276	2010	1.004e-10
GO:BP	GO:0000075	cell cycle checkpoint signaling	50	185	2.185e-10
GO:BP	GO:0043412	macromolecule modification	383	3030	2.719e-10
GO:BP	GO:0090068	positive regulation of cell cycle process	62	262	2.791e-10
GO:BP	GO:0033036	macromolecule localization	403	3228	3.432e-10
GO:BP	GO:0033043	regulation of organelle organization	176	1148	3.496e-10
GO:BP	GO:0051716	cellular response to stimulus	811	7376	4.875e-10
GO:BP	GO:0007010	cytoskeleton organization	218	1529	1.009e-09
GO:BP	GO:0048856	anatomical structure development	676	5997	1.290e-09
GO:BP	GO:0046907	intracellular transport	200	1381	1.971e-09
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	58	248	2.106e-09
GO:BP	GO:0006950	response to stress	472	3948	2.106e-09
GO:BP	GO:0045787	positive regulation of cell cycle	73	351	2.140e-09
GO:BP	GO:0010948	negative regulation of cell cycle process	64	289	2.293e-09
GO:BP	GO:0051310	metaphase chromosome alignment	34	104	2.329e-09
GO:BP	GO:0051983	regulation of chromosome segregation	39	132	2.609e-09
GO:BP	GO:0045786	negative regulation of cell cycle	76	377	3.744e-09
GO:BP	GO:0019222	regulation of metabolic process	771	7035	5.286e-09
GO:BP	GO:0051303	establishment of chromosome localization	36	118	5.324e-09
GO:BP	GO:0051246	regulation of protein metabolic process	250	1855	7.508e-09
GO:BP	GO:0051128	regulation of cellular component organization	312	2433	7.852e-09
GO:BP	GO:0006281	DNA repair	107	621	9.154e-09
GO:BP	GO:0050000	chromosome localization	37	126	9.328e-09
GO:BP	GO:0051252	regulation of RNA metabolic process	441	3687	1.036e-08
GO:BP	GO:0009966	regulation of signal transduction	374	3034	1.083e-08
GO:BP	GO:0048519	negative regulation of biological process	653	5834	1.178e-08
GO:BP	GO:0006355	regulation of DNA-templated transcription	412	3409	1.309e-08
GO:BP	GO:0048523	negative regulation of cellular process	632	5629	1.667e-08
GO:BP	GO:0007399	nervous system development	327	2604	2.643e-08
GO:BP	GO:2001141	regulation of RNA biosynthetic process	412	3428	2.686e-08
GO:BP	GO:0006351	DNA-templated transcription	424	3549	2.983e-08
GO:BP	GO:0044839	cell cycle G2/M phase transition	41	156	3.575e-08
GO:BP	GO:1905818	regulation of chromosome separation	27	77	3.616e-08
GO:BP	GO:1902531	regulation of intracellular signal transduction	257	1953	3.644e-08
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	43	169	3.911e-08
GO:BP	GO:0007088	regulation of mitotic nuclear division	35	121	4.003e-08
GO:BP	GO:0048731	system development	473	4053	5.369e-08
GO:BP	GO:0009893	positive regulation of metabolic process	427	3597	5.535e-08
GO:BP	GO:0006270	DNA replication initiation	18	37	5.838e-08
GO:BP	GO:1903046	meiotic cell cycle process	51	224	6.519e-08
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	51	225	7.471e-08
GO:BP	GO:0060255	regulation of macromolecule metabolic process	710	6492	7.471e-08
GO:BP	GO:0000910	cytokinesis	46	192	7.471e-08
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	321	2578	8.801e-08
GO:BP	GO:0140694	membraneless organelle assembly	79	430	1.099e-07
GO:BP	GO:0006366	transcription by RNA polymerase II	334	2711	1.217e-07
GO:BP	GO:0030154	cell differentiation	508	4437	1.474e-07
GO:BP	GO:0048869	cellular developmental process	508	4438	1.508e-07
GO:BP	GO:0051304	chromosome separation	27	84	2.734e-07
GO:BP	GO:0051321	meiotic cell cycle	60	297	2.743e-07
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	36	136	2.757e-07
GO:BP	GO:0051783	regulation of nuclear division	38	149	3.128e-07
GO:BP	GO:0140013	meiotic nuclear division	46	202	3.830e-07
GO:BP	GO:0015031	protein transport	196	1444	4.337e-07
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	389	3288	5.444e-07
GO:BP	GO:0060341	regulation of cellular localization	147	1013	6.032e-07
GO:BP	GO:0007052	mitotic spindle organization	35	134	6.251e-07
GO:BP	GO:0071705	nitrogen compound transport	247	1923	6.269e-07
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	177	1280	6.328e-07
GO:BP	GO:0007051	spindle organization	46	206	6.885e-07
GO:BP	GO:0006793	phosphorus metabolic process	298	2410	6.992e-07
GO:BP	GO:0051234	establishment of localization	551	4928	7.142e-07
GO:BP	GO:0016310	phosphorylation	181	1320	7.667e-07
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	22	62	8.667e-07
GO:BP	GO:0051640	organelle localization	100	620	8.698e-07
GO:BP	GO:0006796	phosphate-containing compound metabolic process	297	2407	8.807e-07
GO:BP	GO:0006468	protein phosphorylation	170	1227	1.038e-06
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	177	1296	1.449e-06
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	35	139	1.555e-06
GO:BP	GO:0009653	anatomical structure morphogenesis	327	2713	1.616e-06
GO:BP	GO:0000226	microtubule cytoskeleton organization	105	670	1.668e-06
GO:BP	GO:0051253	negative regulation of RNA metabolic process	188	1400	1.754e-06
GO:BP	GO:0007098	centrosome cycle	35	140	1.814e-06
GO:BP	GO:0051098	regulation of binding	46	213	1.814e-06
GO:BP	GO:0042770	signal transduction in response to DNA damage	40	173	2.002e-06
GO:BP	GO:0051306	mitotic sister chromatid separation	22	65	2.113e-06
GO:BP	GO:0061982	meiosis I cell cycle process	35	141	2.150e-06
GO:BP	GO:0050896	response to stimulus	932	8999	2.380e-06
GO:BP	GO:0023052	signaling	699	6515	2.623e-06
GO:BP	GO:0007154	cell communication	701	6540	2.892e-06
GO:BP	GO:0051383	kinetochore organization	12	21	2.941e-06
GO:BP	GO:0048513	animal organ development	363	3085	2.959e-06
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	32	124	2.959e-06
GO:BP	GO:0045184	establishment of protein localization	244	1937	3.454e-06
GO:BP	GO:0034508	centromere complex assembly	14	29	3.609e-06
GO:BP	GO:0009790	embryo development	157	1135	3.675e-06
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	200	1529	4.068e-06
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	20	57	4.087e-06
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	39	172	4.662e-06
GO:BP	GO:0065009	regulation of molecular function	196	1496	4.848e-06
GO:BP	GO:0033044	regulation of chromosome organization	49	242	4.874e-06
GO:BP	GO:0007017	microtubule-based process	141	999	5.176e-06
GO:BP	GO:0031023	microtubule organizing center organization	36	153	5.296e-06
GO:BP	GO:0032880	regulation of protein localization	130	907	6.943e-06
GO:BP	GO:0051099	positive regulation of binding	28	104	7.057e-06
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	20	59	7.449e-06
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	19	54	7.559e-06
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	18	49	7.559e-06
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	18	49	7.559e-06
GO:BP	GO:0071173	spindle assembly checkpoint signaling	18	49	7.559e-06
GO:BP	GO:0031570	DNA integrity checkpoint signaling	31	123	7.559e-06
GO:BP	GO:0051225	spindle assembly	33	136	7.839e-06
GO:BP	GO:0051784	negative regulation of nuclear division	21	65	8.831e-06
GO:BP	GO:0050793	regulation of developmental process	295	2457	1.032e-05
GO:BP	GO:0031577	spindle checkpoint signaling	18	50	1.052e-05
GO:BP	GO:0141124	intracellular signaling cassette	238	1912	1.167e-05
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	251	2036	1.167e-05
GO:BP	GO:0051656	establishment of organelle localization	80	491	1.200e-05
GO:BP	GO:0033045	regulation of sister chromatid segregation	28	107	1.229e-05
GO:BP	GO:0000281	mitotic cytokinesis	26	95	1.257e-05
GO:BP	GO:0030030	cell projection organization	208	1631	1.268e-05
GO:BP	GO:0007127	meiosis I	32	133	1.386e-05
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	18	51	1.386e-05
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	18	51	1.386e-05
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	18	51	1.386e-05
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	18	51	1.386e-05
GO:BP	GO:0071840	cellular component organization or biogenesis	868	8393	1.414e-05
GO:BP	GO:0048583	regulation of response to stimulus	448	3993	1.496e-05
GO:BP	GO:0016043	cellular component organization	848	8184	1.617e-05
GO:BP	GO:0010256	endomembrane system organization	94	613	1.778e-05
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	20	63	2.139e-05
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	202	1588	2.166e-05
GO:BP	GO:0006810	transport	487	4407	2.358e-05
GO:BP	GO:0010638	positive regulation of organelle organization	79	492	2.370e-05
GO:BP	GO:1905819	negative regulation of chromosome separation	18	53	2.517e-05
GO:BP	GO:0051985	negative regulation of chromosome segregation	18	53	2.517e-05
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	18	53	2.517e-05
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	30	124	2.611e-05
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	213	1697	2.634e-05
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	29	118	2.795e-05
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	213	1699	2.839e-05
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	56	312	3.155e-05
GO:BP	GO:0090307	mitotic spindle assembly	22	76	3.215e-05
GO:BP	GO:0035295	tube development	148	1101	3.690e-05
GO:BP	GO:0051984	positive regulation of chromosome segregation	13	30	3.762e-05
GO:BP	GO:0023057	negative regulation of signaling	184	1435	4.059e-05
GO:BP	GO:0009056	catabolic process	309	2639	4.192e-05
GO:BP	GO:0000077	DNA damage checkpoint signaling	28	114	4.192e-05
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	28	114	4.192e-05
GO:BP	GO:0010648	negative regulation of cell communication	184	1436	4.192e-05
GO:BP	GO:0007165	signal transduction	638	6002	4.574e-05
GO:BP	GO:0009411	response to UV	34	155	5.076e-05
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	25	97	6.010e-05
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	303	2593	6.417e-05
GO:BP	GO:0031399	regulation of protein modification process	141	1049	6.436e-05
GO:BP	GO:0051254	positive regulation of RNA metabolic process	225	1835	6.456e-05
GO:BP	GO:0009968	negative regulation of signal transduction	171	1326	6.733e-05
GO:BP	GO:0072331	signal transduction by p53 class mediator	35	164	6.770e-05
GO:BP	GO:0051248	negative regulation of protein metabolic process	99	677	6.801e-05
GO:BP	GO:0022008	neurogenesis	218	1771	7.121e-05
GO:BP	GO:0000727	double-strand break repair via break-induced replication	8	12	7.376e-05
GO:BP	GO:0009888	tissue development	245	2032	7.465e-05
GO:BP	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	26	105	8.031e-05
GO:BP	GO:0016236	macroautophagy	61	362	8.183e-05
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	128	938	8.726e-05
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	24	93	8.880e-05
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	40	202	8.995e-05
GO:BP	GO:2000026	regulation of multicellular organismal development	180	1418	9.156e-05
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	25	100	1.014e-04
GO:BP	GO:0008283	cell population proliferation	242	2015	1.126e-04
GO:BP	GO:0009891	positive regulation of biosynthetic process	311	2696	1.297e-04
GO:BP	GO:0048468	cell development	329	2876	1.333e-04
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	24	96	1.565e-04
GO:BP	GO:0045132	meiotic chromosome segregation	24	96	1.565e-04
GO:BP	GO:0050767	regulation of neurogenesis	62	378	1.592e-04
GO:BP	GO:0000902	cell morphogenesis	133	996	1.637e-04
GO:BP	GO:0006914	autophagy	88	597	1.701e-04
GO:BP	GO:0061919	process utilizing autophagic mechanism	88	597	1.701e-04
GO:BP	GO:0044843	cell cycle G1/S phase transition	43	230	1.725e-04
GO:BP	GO:0097190	apoptotic signaling pathway	89	606	1.729e-04
GO:BP	GO:0032879	regulation of localization	242	2029	1.778e-04
GO:BP	GO:0072359	circulatory system development	149	1145	1.778e-04
GO:BP	GO:0008219	cell death	238	1991	1.824e-04
GO:BP	GO:0007033	vacuole organization	44	239	1.988e-04
GO:BP	GO:0051382	kinetochore assembly	9	17	2.078e-04
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	95	662	2.167e-04
GO:BP	GO:0012501	programmed cell death	237	1987	2.204e-04
GO:BP	GO:0030261	chromosome condensation	15	45	2.252e-04
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	25	105	2.371e-04
GO:BP	GO:0032456	endocytic recycling	22	86	2.437e-04
GO:BP	GO:0006915	apoptotic process	230	1923	2.498e-04
GO:BP	GO:0007417	central nervous system development	139	1061	2.530e-04
GO:BP	GO:0007420	brain development	105	754	2.649e-04
GO:BP	GO:0007507	heart development	88	605	2.703e-04
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	23	93	2.734e-04
GO:BP	GO:0061061	muscle structure development	98	693	2.771e-04
GO:BP	GO:0043687	post-translational protein modification	135	1027	2.838e-04
GO:BP	GO:0032386	regulation of intracellular transport	47	266	2.859e-04
GO:BP	GO:0006275	regulation of DNA replication	27	120	3.053e-04
GO:BP	GO:0033260	nuclear DNA replication	14	41	3.177e-04
GO:BP	GO:0006310	DNA recombination	57	347	3.276e-04
GO:BP	GO:0009057	macromolecule catabolic process	176	1417	3.808e-04
GO:BP	GO:1905820	positive regulation of chromosome separation	12	32	4.614e-04
GO:BP	GO:1903432	regulation of TORC1 signaling	23	96	4.625e-04
GO:BP	GO:0060284	regulation of cell development	114	847	4.964e-04
GO:BP	GO:0038202	TORC1 signaling	24	103	4.964e-04
GO:BP	GO:0044093	positive regulation of molecular function	118	884	5.111e-04
GO:BP	GO:0051101	regulation of DNA binding	19	72	5.889e-04
GO:BP	GO:0007076	mitotic chromosome condensation	9	19	6.012e-04
GO:BP	GO:0045595	regulation of cell differentiation	191	1576	6.897e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	96	692	7.036e-04
GO:BP	GO:0072073	kidney epithelium development	31	154	7.079e-04
GO:BP	GO:0051960	regulation of nervous system development	69	457	7.103e-04
GO:BP	GO:0050790	regulation of catalytic activity	122	928	7.246e-04
GO:BP	GO:0009267	cellular response to starvation	34	177	8.019e-04
GO:BP	GO:0080135	regulation of cellular response to stress	76	519	8.085e-04
GO:BP	GO:0042325	regulation of phosphorylation	111	830	8.110e-04
GO:BP	GO:0010506	regulation of autophagy	58	367	8.286e-04
GO:BP	GO:0060322	head development	108	806	9.534e-04
GO:BP	GO:0001932	regulation of protein phosphorylation	105	779	9.589e-04
GO:BP	GO:0097435	supramolecular fiber organization	114	861	9.638e-04
GO:BP	GO:0032465	regulation of cytokinesis	22	94	9.666e-04
GO:BP	GO:0060395	SMAD protein signal transduction	20	81	9.666e-04
GO:BP	GO:0044786	cell cycle DNA replication	14	45	9.666e-04
GO:BP	GO:0002181	cytoplasmic translation	32	165	1.087e-03
GO:BP	GO:0051239	regulation of multicellular organismal process	329	2956	1.102e-03
GO:BP	GO:0051130	positive regulation of cellular component organization	140	1105	1.104e-03
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	126	975	1.119e-03
GO:BP	GO:0044346	fibroblast apoptotic process	10	25	1.141e-03
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	10	25	1.141e-03
GO:BP	GO:0032501	multicellular organismal process	747	7322	1.141e-03
GO:BP	GO:0000724	double-strand break repair via homologous recombination	35	188	1.141e-03
GO:BP	GO:0006325	chromatin organization	116	884	1.163e-03
GO:BP	GO:0051493	regulation of cytoskeleton organization	75	517	1.173e-03
GO:BP	GO:0006446	regulation of translational initiation	20	83	1.352e-03
GO:BP	GO:0070201	regulation of establishment of protein localization	77	537	1.375e-03
GO:BP	GO:0043009	chordate embryonic development	92	671	1.473e-03
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	53	334	1.512e-03
GO:BP	GO:0007015	actin filament organization	68	461	1.543e-03
GO:BP	GO:0016050	vesicle organization	58	376	1.543e-03
GO:BP	GO:0032970	regulation of actin filament-based process	58	376	1.543e-03
GO:BP	GO:0006412	translation	98	727	1.614e-03
GO:BP	GO:0034198	cellular response to amino acid starvation	15	53	1.628e-03
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	16	59	1.636e-03
GO:BP	GO:0007064	mitotic sister chromatid cohesion	11	31	1.645e-03
GO:BP	GO:1902969	mitotic DNA replication	8	17	1.664e-03
GO:BP	GO:2001252	positive regulation of chromosome organization	23	105	1.804e-03
GO:BP	GO:0000725	recombinational repair	35	193	1.889e-03
GO:BP	GO:0001701	in utero embryonic development	62	413	1.896e-03
GO:BP	GO:1901976	regulation of cell cycle checkpoint	14	48	1.943e-03
GO:BP	GO:1904262	negative regulation of TORC1 signaling	14	48	1.943e-03
GO:BP	GO:0006413	translational initiation	26	127	2.047e-03
GO:BP	GO:0001822	kidney development	51	322	2.073e-03
GO:BP	GO:0008285	negative regulation of cell population proliferation	95	706	2.145e-03
GO:BP	GO:0030029	actin filament-based process	108	825	2.187e-03
GO:BP	GO:0016197	endosomal transport	47	290	2.203e-03
GO:BP	GO:0033365	protein localization to organelle	149	1209	2.213e-03
GO:BP	GO:0072001	renal system development	52	332	2.338e-03
GO:BP	GO:0051302	regulation of cell division	34	188	2.433e-03
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	585	5644	2.437e-03
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	18	74	2.577e-03
GO:BP	GO:1902229	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	12	38	2.644e-03
GO:BP	GO:0030036	actin cytoskeleton organization	97	729	2.681e-03
GO:BP	GO:0061024	membrane organization	107	821	2.731e-03
GO:BP	GO:0009889	regulation of biosynthetic process	600	5809	2.735e-03
GO:BP	GO:0035825	homologous recombination	17	68	2.739e-03
GO:BP	GO:0031647	regulation of protein stability	52	335	2.844e-03
GO:BP	GO:0016192	vesicle-mediated transport	188	1592	2.844e-03
GO:BP	GO:0048585	negative regulation of response to stimulus	197	1680	2.844e-03
GO:BP	GO:0035970	peptidyl-threonine dephosphorylation	7	14	2.844e-03
GO:BP	GO:0016477	cell migration	182	1534	2.844e-03
GO:BP	GO:1990928	response to amino acid starvation	15	56	2.951e-03
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	24	116	3.005e-03
GO:BP	GO:1903829	positive regulation of protein localization	71	499	3.005e-03
GO:BP	GO:0009987	cellular process	1872	20247	3.008e-03
GO:BP	GO:0035967	cellular response to topologically incorrect protein	23	109	3.008e-03
GO:BP	GO:1903025	regulation of RNA polymerase II regulatory region sequence-specific DNA binding	5	7	3.137e-03
GO:BP	GO:0051052	regulation of DNA metabolic process	71	500	3.156e-03
GO:BP	GO:0019220	regulation of phosphate metabolic process	121	956	3.277e-03
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	61	414	3.324e-03
GO:BP	GO:0032006	regulation of TOR signaling	28	146	3.324e-03
GO:BP	GO:0051174	regulation of phosphorus metabolic process	121	957	3.391e-03
GO:BP	GO:0007062	sister chromatid cohesion	15	57	3.529e-03
GO:BP	GO:0032507	maintenance of protein location in cell	15	57	3.529e-03
GO:BP	GO:0048589	developmental growth	89	663	3.529e-03
GO:BP	GO:0031297	replication fork processing	14	51	3.565e-03
GO:BP	GO:0017148	negative regulation of translation	26	132	3.565e-03
GO:BP	GO:0031669	cellular response to nutrient levels	41	248	3.575e-03
GO:BP	GO:2000677	regulation of transcription regulatory region DNA binding	11	34	3.718e-03
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	17	70	3.732e-03
GO:BP	GO:2000269	regulation of fibroblast apoptotic process	8	19	3.777e-03
GO:BP	GO:2001251	negative regulation of chromosome organization	21	97	3.828e-03
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	29	155	3.834e-03
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	107	831	3.986e-03
GO:BP	GO:0007264	small GTPase-mediated signal transduction	71	505	4.064e-03
GO:BP	GO:0051093	negative regulation of developmental process	117	925	4.121e-03
GO:BP	GO:0042127	regulation of cell population proliferation	196	1685	4.247e-03
GO:BP	GO:0030031	cell projection assembly	83	613	4.247e-03
GO:BP	GO:0051247	positive regulation of protein metabolic process	129	1039	4.284e-03
GO:BP	GO:0006886	intracellular protein transport	91	686	4.331e-03
GO:BP	GO:0032835	glomerulus development	17	71	4.348e-03
GO:BP	GO:0022414	reproductive process	188	1608	4.383e-03
GO:BP	GO:0030174	regulation of DNA-templated DNA replication initiation	7	15	4.435e-03
GO:BP	GO:0042594	response to starvation	37	219	4.515e-03
GO:BP	GO:0009314	response to radiation	63	437	4.515e-03
GO:BP	GO:0010468	regulation of gene expression	571	5536	4.601e-03
GO:BP	GO:1902410	mitotic cytokinetic process	11	35	4.717e-03
GO:BP	GO:0034504	protein localization to nucleus	49	318	4.730e-03
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	22	106	4.877e-03
GO:BP	GO:0045995	regulation of embryonic development	20	92	4.877e-03
GO:BP	GO:0071363	cellular response to growth factor stimulus	91	689	4.882e-03
GO:BP	GO:0006302	double-strand break repair	49	319	5.046e-03
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	81	599	5.054e-03
GO:BP	GO:0048858	cell projection morphogenesis	90	681	5.124e-03
GO:BP	GO:0048699	generation of neurons	180	1536	5.176e-03
GO:BP	GO:0044782	cilium organization	62	431	5.202e-03
GO:BP	GO:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	10	30	5.207e-03
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	81	600	5.258e-03
GO:BP	GO:0007034	vacuolar transport	31	174	5.352e-03
GO:BP	GO:0018105	peptidyl-serine phosphorylation	31	174	5.352e-03
GO:BP	GO:0019953	sexual reproduction	137	1122	5.352e-03
GO:BP	GO:0070192	chromosome organization involved in meiotic cell cycle	16	66	5.408e-03
GO:BP	GO:0090231	regulation of spindle checkpoint	9	25	5.471e-03
GO:BP	GO:0031929	TOR signaling	30	167	5.733e-03
GO:BP	GO:0070848	response to growth factor	94	721	5.843e-03
GO:BP	GO:0051223	regulation of protein transport	63	442	5.843e-03
GO:BP	GO:0043388	positive regulation of DNA binding	11	36	5.893e-03
GO:BP	GO:0007041	lysosomal transport	26	137	5.904e-03
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	89	676	6.031e-03
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	18	80	6.031e-03
GO:BP	GO:1990778	protein localization to cell periphery	54	365	6.176e-03
GO:BP	GO:0110020	regulation of actomyosin structure organization	21	101	6.183e-03
GO:BP	GO:0034620	cellular response to unfolded protein	20	94	6.203e-03
GO:BP	GO:0071763	nuclear membrane organization	13	48	6.216e-03
GO:BP	GO:0071495	cellular response to endogenous stimulus	147	1223	6.230e-03
GO:BP	GO:0032446	protein modification by small protein conjugation	108	853	6.276e-03
GO:BP	GO:0016241	regulation of macroautophagy	32	184	6.436e-03
GO:BP	GO:1905821	positive regulation of chromosome condensation	5	8	6.471e-03
GO:BP	GO:0060253	negative regulation of glial cell proliferation	7	16	6.548e-03
GO:BP	GO:0032926	negative regulation of activin receptor signaling pathway	7	16	6.548e-03
GO:BP	GO:0048812	neuron projection morphogenesis	87	660	6.565e-03
GO:BP	GO:0051298	centrosome duplication	17	74	6.586e-03
GO:BP	GO:1902751	positive regulation of cell cycle G2/M phase transition	10	31	6.586e-03
GO:BP	GO:1900180	regulation of protein localization to nucleus	27	146	6.727e-03
GO:BP	GO:0065004	protein-DNA complex assembly	39	241	6.855e-03
GO:BP	GO:2000737	negative regulation of stem cell differentiation	9	26	7.230e-03
GO:BP	GO:0032007	negative regulation of TOR signaling	16	68	7.279e-03
GO:BP	GO:0022616	DNA strand elongation	11	37	7.279e-03
GO:BP	GO:0043174	nucleoside salvage	6	12	7.351e-03
GO:BP	GO:0006997	nucleus organization	27	147	7.421e-03
GO:BP	GO:0007163	establishment or maintenance of cell polarity	38	234	7.460e-03
GO:BP	GO:0072595	maintenance of protein localization in organelle	12	43	7.488e-03
GO:BP	GO:0018209	peptidyl-serine modification	32	186	7.534e-03
GO:BP	GO:0061572	actin filament bundle organization	29	163	7.880e-03
GO:BP	GO:0044087	regulation of cellular component biogenesis	124	1011	8.024e-03
GO:BP	GO:0035239	tube morphogenesis	110	879	8.143e-03
GO:BP	GO:0061036	positive regulation of cartilage development	10	32	8.478e-03
GO:BP	GO:0006417	regulation of translation	55	380	8.832e-03
GO:BP	GO:0032506	cytokinetic process	13	50	8.992e-03
GO:BP	GO:0031032	actomyosin structure organization	35	212	8.992e-03
GO:BP	GO:0034644	cellular response to UV	19	90	9.023e-03
GO:BP	GO:0018193	peptidyl-amino acid modification	89	686	9.033e-03
GO:BP	GO:0048863	stem cell differentiation	39	245	9.179e-03
GO:BP	GO:0071824	protein-DNA complex organization	41	262	9.488e-03
GO:BP	GO:0048729	tissue morphogenesis	81	614	9.594e-03
GO:BP	GO:0034349	glial cell apoptotic process	7	17	9.594e-03
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	143	1199	9.702e-03
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	27	150	9.887e-03
GO:BP	GO:0071214	cellular response to abiotic stimulus	50	339	9.936e-03
GO:BP	GO:0104004	cellular response to environmental stimulus	50	339	9.936e-03
GO:BP	GO:0061709	reticulophagy	8	22	9.990e-03
GO:BP	GO:0001738	morphogenesis of a polarized epithelium	14	57	9.990e-03
GO:BP	GO:0010498	proteasomal protein catabolic process	73	543	1.028e-02
GO:BP	GO:0051338	regulation of transferase activity	68	498	1.028e-02
GO:BP	GO:0045596	negative regulation of cell differentiation	87	671	1.031e-02
GO:BP	GO:0007040	lysosome organization	22	113	1.049e-02
GO:BP	GO:0080171	lytic vacuole organization	22	113	1.049e-02
GO:BP	GO:0035051	cardiocyte differentiation	27	151	1.075e-02
GO:BP	GO:0030163	protein catabolic process	125	1030	1.091e-02
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	12	45	1.103e-02
GO:BP	GO:0031503	protein-containing complex localization	35	215	1.112e-02
GO:BP	GO:0090232	positive regulation of spindle checkpoint	6	13	1.160e-02
GO:BP	GO:0043393	regulation of protein binding	22	114	1.173e-02
GO:BP	GO:0032786	positive regulation of DNA-templated transcription, elongation	14	58	1.173e-02
GO:BP	GO:0000912	assembly of actomyosin apparatus involved in cytokinesis	5	9	1.184e-02
GO:BP	GO:0048666	neuron development	140	1177	1.184e-02
GO:BP	GO:0000915	actomyosin contractile ring assembly	5	9	1.184e-02
GO:BP	GO:0000301	retrograde transport, vesicle recycling within Golgi	5	9	1.184e-02
GO:BP	GO:0070255	regulation of mucus secretion	5	9	1.184e-02
GO:BP	GO:0051017	actin filament bundle assembly	28	160	1.188e-02
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	30	176	1.214e-02
GO:BP	GO:0030182	neuron differentiation	168	1451	1.217e-02
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	148	1256	1.228e-02
GO:BP	GO:0045185	maintenance of protein location	15	65	1.233e-02
GO:BP	GO:0060429	epithelium development	146	1238	1.283e-02
GO:BP	GO:0042692	muscle cell differentiation	57	405	1.293e-02
GO:BP	GO:1902115	regulation of organelle assembly	37	234	1.333e-02
GO:BP	GO:0043149	stress fiber assembly	21	108	1.343e-02
GO:BP	GO:0060412	ventricular septum morphogenesis	11	40	1.343e-02
GO:BP	GO:0030038	contractile actin filament bundle assembly	21	108	1.343e-02
GO:BP	GO:0006998	nuclear envelope organization	14	59	1.356e-02
GO:BP	GO:0030323	respiratory tube development	33	202	1.411e-02
GO:BP	GO:0048144	fibroblast proliferation	21	109	1.511e-02
GO:BP	GO:0072009	nephron epithelium development	23	124	1.511e-02
GO:BP	GO:0048193	Golgi vesicle transport	46	312	1.522e-02
GO:BP	GO:0007131	reciprocal meiotic recombination	14	60	1.597e-02
GO:BP	GO:0140527	reciprocal homologous recombination	14	60	1.597e-02
GO:BP	GO:0055007	cardiac muscle cell differentiation	22	117	1.597e-02
GO:BP	GO:0007517	muscle organ development	52	365	1.599e-02
GO:BP	GO:0031175	neuron projection development	123	1023	1.599e-02
GO:BP	GO:0018205	peptidyl-lysine modification	25	140	1.606e-02
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	19	95	1.617e-02
GO:BP	GO:0045143	homologous chromosome segregation	15	67	1.655e-02
GO:BP	GO:0034137	positive regulation of toll-like receptor 2 signaling pathway	4	6	1.717e-02
GO:BP	GO:0070257	positive regulation of mucus secretion	4	6	1.717e-02
GO:BP	GO:0010032	meiotic chromosome condensation	4	6	1.717e-02
GO:BP	GO:0051231	spindle elongation	6	14	1.725e-02
GO:BP	GO:0090235	regulation of metaphase plate congression	6	14	1.725e-02
GO:BP	GO:0009416	response to light stimulus	47	323	1.732e-02
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	8	24	1.737e-02
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	8	24	1.737e-02
GO:BP	GO:0034502	protein localization to chromosome	23	126	1.824e-02
GO:BP	GO:0009163	nucleoside biosynthetic process	7	19	1.833e-02
GO:BP	GO:0034404	nucleobase-containing small molecule biosynthetic process	7	19	1.833e-02
GO:BP	GO:1901978	positive regulation of cell cycle checkpoint	7	19	1.833e-02
GO:BP	GO:0031344	regulation of cell projection organization	84	658	1.833e-02
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	14	61	1.833e-02
GO:BP	GO:0032092	positive regulation of protein binding	12	48	1.854e-02
GO:BP	GO:0001824	blastocyst development	22	119	1.926e-02
GO:BP	GO:0002009	morphogenesis of an epithelium	67	503	1.926e-02
GO:BP	GO:0006338	chromatin remodeling	91	725	1.938e-02
GO:BP	GO:0071478	cellular response to radiation	30	182	1.943e-02
GO:BP	GO:0009967	positive regulation of signal transduction	179	1578	1.944e-02
GO:BP	GO:0031055	chromatin remodeling at centromere	5	10	1.968e-02
GO:BP	GO:0044837	actomyosin contractile ring organization	5	10	1.968e-02
GO:BP	GO:0009894	regulation of catabolic process	124	1040	1.968e-02
GO:BP	GO:0034080	CENP-A containing chromatin assembly	5	10	1.968e-02
GO:BP	GO:0072659	protein localization to plasma membrane	43	291	1.970e-02
GO:BP	GO:0046825	regulation of protein export from nucleus	10	36	1.972e-02
GO:BP	GO:0010639	negative regulation of organelle organization	50	352	1.987e-02
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	82	642	1.987e-02
GO:BP	GO:0050821	protein stabilization	35	224	2.060e-02
GO:BP	GO:0032147	activation of protein kinase activity	14	62	2.089e-02
GO:BP	GO:0030010	establishment of cell polarity	27	159	2.094e-02
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	17	83	2.100e-02
GO:BP	GO:0021537	telencephalon development	42	284	2.164e-02
GO:BP	GO:0060541	respiratory system development	35	225	2.207e-02
GO:BP	GO:0048870	cell motility	200	1793	2.212e-02
GO:BP	GO:0032925	regulation of activin receptor signaling pathway	8	25	2.216e-02
GO:BP	GO:0072006	nephron development	27	160	2.276e-02
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	131	1113	2.292e-02
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	33	209	2.294e-02
GO:BP	GO:0051492	regulation of stress fiber assembly	18	91	2.294e-02
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	51	364	2.354e-02
GO:BP	GO:0023056	positive regulation of signaling	200	1796	2.363e-02
GO:BP	GO:0071539	protein localization to centrosome	10	37	2.394e-02
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	10	37	2.394e-02
GO:BP	GO:0018107	peptidyl-threonine phosphorylation	16	77	2.400e-02
GO:BP	GO:0009628	response to abiotic stimulus	134	1144	2.400e-02
GO:BP	GO:0044771	meiotic cell cycle phase transition	6	15	2.410e-02
GO:BP	GO:1902166	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	6	15	2.410e-02
GO:BP	GO:2000679	positive regulation of transcription regulatory region DNA binding	7	20	2.410e-02
GO:BP	GO:0006271	DNA strand elongation involved in DNA replication	6	15	2.410e-02
GO:BP	GO:0000076	DNA replication checkpoint signaling	7	20	2.410e-02
GO:BP	GO:0065008	regulation of biological quality	313	2947	2.420e-02
GO:BP	GO:0001568	blood vessel development	91	732	2.423e-02
GO:BP	GO:1902903	regulation of supramolecular fiber organization	53	383	2.472e-02
GO:BP	GO:0035850	epithelial cell differentiation involved in kidney development	12	50	2.493e-02
GO:BP	GO:0032924	activin receptor signaling pathway	12	50	2.493e-02
GO:BP	GO:0032968	positive regulation of transcription elongation by RNA polymerase II	12	50	2.493e-02
GO:BP	GO:0032467	positive regulation of cytokinesis	12	50	2.493e-02
GO:BP	GO:0060173	limb development	31	194	2.499e-02
GO:BP	GO:0048736	appendage development	31	194	2.499e-02
GO:BP	GO:0003176	aortic valve development	11	44	2.713e-02
GO:BP	GO:1903008	organelle disassembly	15	71	2.723e-02
GO:BP	GO:0001503	ossification	58	430	2.749e-02
GO:BP	GO:1905207	regulation of cardiocyte differentiation	8	26	2.787e-02
GO:BP	GO:1905508	protein localization to microtubule organizing center	10	38	2.865e-02
GO:BP	GO:0043549	regulation of kinase activity	58	431	2.885e-02
GO:BP	GO:0034599	cellular response to oxidative stress	37	247	3.045e-02
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	16	79	3.048e-02
GO:BP	GO:0051256	mitotic spindle midzone assembly	5	11	3.048e-02
GO:BP	GO:0035329	hippo signaling	13	58	3.070e-02
GO:BP	GO:0035148	tube formation	25	148	3.110e-02
GO:BP	GO:0062197	cellular response to chemical stress	45	317	3.173e-02
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	7	21	3.189e-02
GO:BP	GO:1905684	regulation of plasma membrane repair	4	7	3.198e-02
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	4	7	3.198e-02
GO:BP	GO:2000270	negative regulation of fibroblast apoptotic process	4	7	3.198e-02
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	11	45	3.199e-02
GO:BP	GO:0042177	negative regulation of protein catabolic process	21	117	3.206e-02
GO:BP	GO:0031214	biomineral tissue development	29	181	3.227e-02
GO:BP	GO:0018210	peptidyl-threonine modification	17	87	3.274e-02
GO:BP	GO:0031401	positive regulation of protein modification process	80	637	3.277e-02
GO:BP	GO:0048313	Golgi inheritance	6	16	3.328e-02
GO:BP	GO:0070254	mucus secretion	6	16	3.328e-02
GO:BP	GO:0048308	organelle inheritance	6	16	3.328e-02
GO:BP	GO:0098877	neurotransmitter receptor transport to plasma membrane	6	16	3.328e-02
GO:BP	GO:0030324	lung development	31	198	3.328e-02
GO:BP	GO:0003007	heart morphogenesis	39	266	3.339e-02
GO:BP	GO:0060562	epithelial tube morphogenesis	47	336	3.345e-02
GO:BP	GO:0007585	respiratory gaseous exchange by respiratory system	16	80	3.345e-02
GO:BP	GO:2000736	regulation of stem cell differentiation	16	80	3.345e-02
GO:BP	GO:0055013	cardiac muscle cell development	16	80	3.345e-02
GO:BP	GO:0046677	response to antibiotic	10	39	3.365e-02
GO:BP	GO:0014706	striated muscle tissue development	55	408	3.417e-02
GO:BP	GO:0003281	ventricular septum development	15	73	3.427e-02
GO:BP	GO:0061005	cell differentiation involved in kidney development	13	59	3.449e-02
GO:BP	GO:0000045	autophagosome assembly	21	118	3.455e-02
GO:BP	GO:0006767	water-soluble vitamin metabolic process	14	66	3.458e-02
GO:BP	GO:0043094	metabolic compound salvage	9	33	3.461e-02
GO:BP	GO:0061842	microtubule organizing center localization	9	33	3.461e-02
GO:BP	GO:0051642	centrosome localization	9	33	3.461e-02
GO:BP	GO:0051147	regulation of muscle cell differentiation	24	142	3.557e-02
GO:BP	GO:0032231	regulation of actin filament bundle assembly	19	103	3.561e-02
GO:BP	GO:0014896	muscle hypertrophy	17	88	3.565e-02
GO:BP	GO:0000165	MAPK cascade	91	744	3.573e-02
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	331	3157	3.573e-02
GO:BP	GO:0031667	response to nutrient levels	66	510	3.621e-02
GO:BP	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	11	46	3.642e-02
GO:BP	GO:0022411	cellular component disassembly	59	446	3.642e-02
GO:BP	GO:0002183	cytoplasmic translational initiation	11	46	3.642e-02
GO:BP	GO:0045597	positive regulation of cell differentiation	105	879	3.674e-02
GO:BP	GO:0003231	cardiac ventricle development	22	127	3.803e-02
GO:BP	GO:0051403	stress-activated MAPK cascade	12	53	3.836e-02
GO:BP	GO:0045859	regulation of protein kinase activity	54	402	3.882e-02
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	10	40	3.958e-02
GO:BP	GO:1902117	positive regulation of organelle assembly	17	89	3.958e-02
GO:BP	GO:1902254	negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator	7	22	3.970e-02
GO:BP	GO:1905146	lysosomal protein catabolic process	7	22	3.970e-02
GO:BP	GO:0045947	negative regulation of translational initiation	7	22	3.970e-02
GO:BP	GO:0060271	cilium assembly	54	403	4.052e-02
GO:BP	GO:0021915	neural tube development	26	160	4.079e-02
GO:BP	GO:0033157	regulation of intracellular protein transport	25	152	4.120e-02
GO:BP	GO:0051129	negative regulation of cellular component organization	86	701	4.127e-02
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	114	970	4.127e-02
GO:BP	GO:0009892	negative regulation of metabolic process	351	3375	4.189e-02
GO:BP	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	8	28	4.189e-02
GO:BP	GO:0070168	negative regulation of biomineral tissue development	8	28	4.189e-02
GO:BP	GO:0036296	response to increased oxygen levels	8	28	4.189e-02
GO:BP	GO:0015833	peptide transport	41	288	4.206e-02
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	28	177	4.214e-02
GO:BP	GO:0061512	protein localization to cilium	15	75	4.218e-02
GO:BP	GO:0010647	positive regulation of cell communication	197	1795	4.218e-02
GO:BP	GO:1905636	positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding	3	4	4.218e-02
GO:BP	GO:2000689	actomyosin contractile ring assembly actin filament organization	3	4	4.218e-02
GO:BP	GO:0006404	RNA import into nucleus	3	4	4.218e-02
GO:BP	GO:0000422	autophagy of mitochondrion	19	105	4.218e-02
GO:BP	GO:0000022	mitotic spindle elongation	5	12	4.237e-02
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	5	12	4.237e-02
GO:BP	GO:0099515	actin filament-based transport	5	12	4.237e-02
GO:BP	GO:0090267	positive regulation of mitotic cell cycle spindle assembly checkpoint	5	12	4.237e-02
GO:BP	GO:0072178	nephric duct morphogenesis	5	12	4.237e-02
GO:BP	GO:0060623	regulation of chromosome condensation	5	12	4.237e-02
GO:BP	GO:0051081	nuclear membrane disassembly	5	12	4.237e-02
GO:BP	GO:0030900	forebrain development	56	423	4.279e-02
GO:BP	GO:1902165	regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	6	17	4.279e-02
GO:BP	GO:0046605	regulation of centrosome cycle	12	54	4.279e-02
GO:BP	GO:0002062	chondrocyte differentiation	21	121	4.332e-02
GO:BP	GO:0043408	regulation of MAPK cascade	79	637	4.338e-02
GO:BP	GO:0003300	cardiac muscle hypertrophy	16	83	4.476e-02
GO:BP	GO:0019941	modification-dependent protein catabolic process	79	638	4.506e-02
GO:BP	GO:0006913	nucleocytoplasmic transport	46	334	4.507e-02
GO:BP	GO:0051169	nuclear transport	46	334	4.507e-02
GO:BP	GO:0042063	gliogenesis	48	352	4.515e-02
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	10	41	4.515e-02
GO:BP	GO:0009306	protein secretion	51	379	4.515e-02
GO:BP	GO:0001944	vasculature development	92	762	4.530e-02
GO:BP	GO:0003333	amino acid transmembrane transport	19	106	4.542e-02
GO:BP	GO:0048598	embryonic morphogenesis	77	620	4.609e-02
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	51	380	4.734e-02
GO:BP	GO:0003013	circulatory system process	75	602	4.758e-02
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	14	69	4.770e-02
GO:BP	GO:0060411	cardiac septum morphogenesis	14	69	4.770e-02
GO:BP	GO:1905314	semi-lunar valve development	11	48	4.770e-02
GO:BP	GO:1901797	negative regulation of signal transduction by p53 class mediator	9	35	4.814e-02
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	12	55	4.848e-02
GO:BP	GO:0003177	pulmonary valve development	7	23	4.848e-02
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	7	23	4.848e-02
GO:BP	GO:0044380	protein localization to cytoskeleton	13	62	4.848e-02
GO:BP	GO:0007409	axonogenesis	60	463	4.853e-02
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	74	594	4.968e-02
KEGG	KEGG:04110	Cell cycle	50	157	3.797e-10
KEGG	KEGG:04218	Cellular senescence	35	155	3.019e-03
KEGG	KEGG:04114	Oocyte meiosis	31	131	3.019e-03
KEGG	KEGG:04390	Hippo signaling pathway	34	157	6.590e-03
KEGG	KEGG:05222	Small cell lung cancer	23	92	8.018e-03
KEGG	KEGG:04115	p53 signaling pathway	19	74	1.773e-02
KEGG	KEGG:04392	Hippo signaling pathway - multiple species	10	29	3.479e-02
KEGG	KEGG:05165	Human papillomavirus infection	55	330	4.481e-02
KEGG	KEGG:03030	DNA replication	11	36	4.679e-02

#GO:BP
table_unassign_genes_GOBP <- table_unassign_GOKEGG_genes %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_unassign_genes_GOBP %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Unassigned Enriched GO:BP Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif Unassigned Gene Set-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#KEGG
table_unassign_genes_KEGG <- table_unassign_GOKEGG_genes %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_unassign_genes_KEGG %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("Cormotif Unassigned DEGs Enriched KEGG Terms")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "Cormotif Unassigned Gene Set-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Cormotif RUVs Corrected Norm Counts TMM and log2cpm

# #read in the norm counts df (normalized counts from RUV)
set1 <- readRDS("data/new/RUV/set1_RUVsk1_normcounts.RDS")
NormCounts_RUV_rep <- as.data.frame(set1$normalizedCounts)
# 
# #read in my metadata sheet that I'll use as the standard for labelling
# #this one already has the replicate individual removed
Metadata_2 <- readRDS("data/new/Metadata_2_norep.RDS")
# 
# #I'll have to remove the replicate at this stage so I can properly run Cormotif
NormCounts_RUV <- NormCounts_RUV_rep %>%
  dplyr::select(-(contains("6R")))
# 
# #now ensure the column names match the original dge$counts with Sample_name
colnames(NormCounts_RUV) <- Metadata_2$Sample_name
# 
# #now, make this into a dge object as I did for DE + Cormotif
dge_RUV <- DGEList(counts = NormCounts_RUV)
# 
# #put the Condition names as a factor onto the dge object for further sorting
dge_RUV$samples$group <- factor(Metadata_2[colnames(NormCounts_RUV), "Condition"])
# 
# #TMM normalize the normalized counts input with the dge object
dge_RUV_calc <- calcNormFactors(dge_RUV, method = "TMM")

Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced
Warning in .calcFactorTMM(obs = x[, i], ref = x[, refColumn], libsize.obs =
lib.size[i], : NaNs produced

# #this is producing a lot of NaNs warnings, perhaps because TMM should occur before norm counts?
# 
# #try by performing TMM normalization before norm counts in set1
# 
counts <- readRDS("data/new/RUV/filt_counts_matrix.RDS")
# #use this counts file to feed into set1 - but instead TMM normalize it first
# 
counts_tmm <- calcNormFactors(counts, method = "TMM")
# 
# set1_tmm <- RUVSeq::RUVs(x = counts_tmm, k =1, scIdx = scIdx, isLog = FALSE)
# error with tmm normalized counts going into RUVseq
# 
# summary(colSums(NormCounts_RUV))
# dge_RUV$samples
# # 
ncol(NormCounts_RUV) == nrow(Metadata_2)           # Should be TRUE

[1] TRUE

all(colnames(NormCounts_RUV) == rownames(Metadata_2))

[1] TRUE

# 
# 
# #save this file so I can read it in later!
# #saveRDS(dge_RUV_calc, "data/new/Cormotif/dge_matrix_forCormotif.RDS")
# 
# #check normalization factors from TMM normalization of LIBRARIES
# dge_RUV_calc$samples
# #it was normalized properly but generated NaNs warnings?
# #still has the same number of columns, properly labelled and in order according to metadata
#  #should be okay - let's try running it and see if it works properly
# 
# Metadata_2_ordered <- Metadata_2[match(colnames(NormCounts_RUV), Metadata_2$Sample_name), ]
# 
# #now cpm these TMM normalized norm counts
# cmf_RUV_cpm <- cpm(dge_RUV_calc, log = TRUE)
# 
# #change the column names to match the Metadata sheet I have
# colnames(cmf_RUV_cpm) <- (Metadata_2$Final_sample_name)
# 
# cmf_RUV_counts <- dge_RUV_calc
# 
# #now make your TMM normalized cpm of norm counts into a dataframe + add Entrez_ID as a col
# cmf_RUV_df <- cmf_RUV_cpm %>%
  # as.data.frame() %>%
  # rownames_to_column(., var = "Entrez_ID")
# 
# #save this to a csv file so I can reorder this matrix easily
# #write.csv(cmf_RUV_cpm, "data/new/Cormotif/RUV/Cormotif_RUVk1_cpm_matrix.csv")
# 
# #reorder my test matrix to match the new groupid I've made
# #I want my columns to be in this order:
# #DOX24T 1-6, DOX24R 1-6, DOX144R 1-6, DMSO24T 1-6, DMSO24R 1-6, DMSO144R 1-6
# Cormotif_RUV <- read.csv("data/new/cmf_RUV_final.csv")
# dim(Cormotif_RUV)
# # #14319 genes across 37 cols (1 is Entrez_ID)
# Cormotif_RUV_df <- data.frame(Cormotif_RUV)
# # 
# rownames(Cormotif_RUV_df) <- Cormotif_RUV_df$Entrez_ID
# exprs.cmf_RUV <- as.matrix(Cormotif_RUV_df[,2:37])
# dim(exprs.cmf_RUV)
# # 
# 
# #put together my group id and comparison id to make the correct comparisons between experimental conditions
# 
# #groupid tells which experimental conditions are grouped together
# #compid tells which experimental conditions should be compared against one another
# ##ie DOX24T vs DMSO24T matched control
# 
# groupid <- c(
#   DOX_24T_1 = 1,
#   DOX_24T_2 = 1,
#   DOX_24T_3 = 1,
#   DOX_24T_4 = 1,
#   DOX_24T_5 = 1,
#   DOX_24T_6 = 1,
#   DOX_24R_1 = 2,
#   DOX_24R_2 = 2,
#   DOX_24R_3 = 2,
#   DOX_24R_4 = 2,
#   DOX_24R_5 = 2,
#   DOX_24R_6 = 2,
#   DOX_144R_1 = 3,
#   DOX_144R_2 = 3,
#   DOX_144R_3 = 3,
#   DOX_144R_4 = 3,
#   DOX_144R_5 = 3,
#   DOX_144R_6 = 3,
#   DMSO_24T_1 = 4,
#   DMSO_24T_2 = 4,
#   DMSO_24T_3 = 4,
#   DMSO_24T_4 = 4,
#   DMSO_24T_5 = 4,
#   DMSO_24T_6 = 4,
#   DMSO_24R_1 = 5,
#   DMSO_24R_2 = 5,
#   DMSO_24R_3 = 5,
#   DMSO_24R_4 = 5,
#   DMSO_24R_5 = 5,
#   DMSO_24R_6 = 5,
#   DMSO_144R_1 = 6,
#   DMSO_144R_2 = 6,
#   DMSO_144R_3 = 6,
#   DMSO_144R_4 = 6,
#   DMSO_144R_5 = 6,
#   DMSO_144R_6 = 6
# )
# #saveRDS(groupid, "data/new/groupidCormotif.RDS")
# 
# compid <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))
# #saveRDS(compid, "data/new/compidCormotif.RDS")

##RUVs Cormotif TMM norm counts

#raw counts file
counts <- readRDS("data/new/RUV/filt_counts_matrix.RDS")

#create a dgelist object from these counts
dge_test <- DGEList(counts = counts)
dim(dge_test$counts)

[1] 14319    42

#14319 genes as normal, still contains replicate needed for RUVs

#apply TMM normalization to this DGElist object
dge_test_tmm <- calcNormFactors(object = dge_test, method = "TMM")
#this ran through just fine, must be something to do with applying TMM to normalized counts
dim(dge_test_tmm$counts)

[1] 14319    42

#14319 genes as normal, still have the replicate so 42 cols
#this still has the entrez_id so I should probably make sure that this is carried down

#pass this TMM normalized DGElist into RUVs correction
colnames(dge_test_tmm) <- Metadata$Final_sample_name
dim(dge_test_tmm)

[1] 14319    42

#14319 genes as normal


RUV_filt_counts_tmm <- dge_test_tmm$counts %>% 
  as.data.frame() 

Entrez_ID_tmm_RUV <- RUV_filt_counts_tmm$Entrez_ID
# saveRDS(Entrez_ID_tmm_RUV, "data/new/RUV/entrezID_tmm_RUV_list.RDS")

dim(RUV_filt_counts_tmm)

[1] 14319    42

#14319 genes as normal, no need to add the filtering step as the counts are already filtered

#add in the annotation files
ind_num <- readRDS("data/new/ind_num.RDS")
annot <- read.csv("data/new/Metadata.csv")

#counts need to be integer values and in a numeric matrix
#note: the log transformation needs to be accounted for in the isLog argument in RUVs function.
counts_test_tmm <- as.matrix(RUV_filt_counts_tmm)
#saveRDS(counts_test_tmm, "data/new/RUV/counts_tmm_filtered.RDS")

# Create a DataFrame for the phenoData
phenoData <- DataFrame(annot)

# Now create the RangedSummarizedExperiment necessary for RUVs input
# looks like it did need both the phenodata and the counts.
set_tmm <- SummarizedExperiment(assays = counts_test_tmm, metadata = phenoData)
dim(set_tmm)

[1] 14319    42

#14319 genes as before

# Generate a background matrix
# The column "Cond" holds the comparisons that you actually want to make. DOX_24, DMSO_24,5FU_24, DOX_3,etc.
scIdx <-RUVSeq::makeGroups(phenoData$Condition)
scIdx

     [,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,]    6   12   18   24   30   36   42
[2,]    4   10   16   22   28   34   40
[3,]    2    8   14   20   26   32   38
[4,]    5   11   17   23   29   35   41
[5,]    3    9   15   21   27   33   39
[6,]    1    7   13   19   25   31   37

#now run through RUV correction with my tmm normalized data to generate normalized counts
set1_tmm <- RUVSeq::RUVs(x = counts_test_tmm, k =1, scIdx = scIdx, isLog = FALSE)
dim(set1_tmm$normalizedCounts)

[1] 14319    42

#14319 genes as before, still containing the replicate individual

#saveRDS(set1_tmm, "data/new/RUV/set1_TMMnorm_RUVsk1_normcounts.RDS")

#make a df of the data for Cormotif?
RUV_df1_tmm <- set1_tmm$W %>% as.data.frame()
RUV_df1_tmm$Names <- rownames(RUV_df1_tmm)

#ensure that the names match across samples
RUV_df_rm1_tmm <- RUV_df1_tmm[RUV_df1_tmm$Names %in% annot$Final_sample_name, ] 
RUV_1_tmm <-  RUV_df_rm1_tmm$W_1

#now that I've passed my TMM normalized counts into the set_tmm, proceed to Cormotif

#####Cormotif Data Setup#####
set1_tmm <- readRDS("data/new/RUV/set1_TMMnorm_RUVsk1_normcounts.RDS")
NormCounts_RUV_rep <- as.data.frame(set1_tmm$normalizedCounts)

#read in my metadata sheet that I'll use as the standard for labelling
#this one already has the replicate individual removed
Metadata_2 <- readRDS("data/new/Metadata_2_norep.RDS")

#I'll have to remove the replicate at this stage so I can properly run Cormotif
NormCounts_RUV <- NormCounts_RUV_rep %>% 
  dplyr::select(-(contains("6R")))
#14319 genes and 36 columns, the right size matrix for Cormotif

#now ensure the column names match the original dge$counts with Sample_name
colnames(NormCounts_RUV) <- Metadata_2$Sample_name
rownames(NormCounts_RUV) <- Entrez_ID_tmm_RUV

#now cpm the cormotif matrix you're going to use
##this should be tmm normalized log2cpm at the end for going into Cormotif
cmf_test <- cpm(NormCounts_RUV, log = TRUE)
colnames(cmf_test) <- (Metadata_2$Final_sample_name)

cmf_counts <- dge_test_tmm$counts %>% 
  as.data.frame() %>% 
  dplyr::select(-(contains("6R")))

cmf_test_df <- cmf_test %>% 
  as.data.frame() %>% 
  rownames_to_column(., var = "Entrez_ID")

#write.csv(x = cmf_test, file = "data/new/RUV/cormotif_test_matrix_TMMnorm.csv")

#reorder my test matrix to match the new groupid I've made
#I want my columns to be in this order:
#DOX24T 1-6, DOX24R 1-6, DOX144R 1-6, DMSO24T 1-6, DMSO24R 1-6, DMSO144R 1-6
Cormotif_ruv <- read.csv("data/new/RUV/Cormotif_RUV_final.csv")
dim(Cormotif_ruv)

[1] 14319    37

#14319 genes across 37 cols (1 is Entrez_ID)
Cormotif_ruv_df <- data.frame(Cormotif_ruv)

rownames(Cormotif_ruv_df) <- Cormotif_ruv_df$Entrez_ID
exprs.cmf_ruv <- as.matrix(Cormotif_ruv_df[,2:37])
dim(exprs.cormotif)

[1] 14319    36

#14319 genes in 36 columns, set up for plugging into Cormotif

#now I need to set up my groupid and compid accordingly

#put together my group id and comparison id to make the correct comparisons between experimental conditions

#groupid tells which experimental conditions are grouped together
#compid tells which experimental conditions should be compared against one another
##ie DOX24T vs DMSO24T matched control

groupid_csv <- read.csv("data/new/GroupID.csv")
#now I have to make this into a vector (named vector)?
groupid <- c(
  DOX_24T_1 = 1, 
  DOX_24T_2 = 1, 
  DOX_24T_3 = 1, 
  DOX_24T_4 = 1, 
  DOX_24T_5 = 1, 
  DOX_24T_6 = 1,
  DOX_24R_1 = 2, 
  DOX_24R_2 = 2, 
  DOX_24R_3 = 2, 
  DOX_24R_4 = 2, 
  DOX_24R_5 = 2, 
  DOX_24R_6 = 2,
  DOX_144R_1 = 3, 
  DOX_144R_2 = 3, 
  DOX_144R_3 = 3, 
  DOX_144R_4 = 3, 
  DOX_144R_5 = 3, 
  DOX_144R_6 = 3,
  DMSO_24T_1 = 4, 
  DMSO_24T_2 = 4, 
  DMSO_24T_3 = 4, 
  DMSO_24T_4 = 4, 
  DMSO_24T_5 = 4, 
  DMSO_24T_6 = 4,
  DMSO_24R_1 = 5, 
  DMSO_24R_2 = 5, 
  DMSO_24R_3 = 5, 
  DMSO_24R_4 = 5, 
  DMSO_24R_5 = 5, 
  DMSO_24R_6 = 5,
  DMSO_144R_1 = 6, 
  DMSO_144R_2 = 6, 
  DMSO_144R_3 = 6, 
  DMSO_144R_4 = 6, 
  DMSO_144R_5 = 6, 
  DMSO_144R_6 = 6
)
#saveRDS(groupid, "data/new/groupidCormotif.RDS")

compid <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))
#saveRDS(compid, "data/new/compidCormotif.RDS")
compid_cmf <- readRDS("data/new/compidCormotif.RDS")

###Run Cormotif RUVs TMM Norm Counts

#set the seed the same as the previous one to ensure consistency

#fit Cormotif model
# set.seed(19191)
#only set the seed ONCE
# 
# motif.fitted_ruv <- cormotiffit(
#   exprs = exprs.cmf_ruv,
#   groupid = groupid_csv,
#   compid = compid_cmf,
#   K = 1:10,
#   max.iter = 1000,
#   BIC = TRUE,
#   runtype = "logCPM"
# )

# saveRDS(motif.fitted_RUV, "data/new/RUV/motif.fitted_ruv_250624.RDS")
motif.fitted_RUV <- readRDS("data/new/RUV/motif.fitted_ruv_250624.RDS")

###Plot TMM Norm Counts RUVs Cormotif

#plot BIC and AIC to see which number of motifs was best for both models
plotIC(motif.fitted_RUV)

Past versions of "RUVs Cormotif Plots-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

motif.fitted_RUV$bic

       K      bic
 [1,]  1 227112.8
 [2,]  2 226776.5
 [3,]  3 226811.1
 [4,]  4 226849.7
 [5,]  5 226888.4
 [6,]  6 226927.1
 [7,]  7 226965.9
 [8,]  8 227004.3
 [9,]  9 227043.6
[10,] 10 227082.0

#now plot the motifs themselves
plotMotif(motif.fitted_RUV, title = "Fitted Motifs for DXR RUVs")

Past versions of "RUVs Cormotif Plots-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#plot the probability legend
myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "RUVs Cormotif Plots-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

##Cormotif RUVs no TMM

#plot the AIC and BIC (we're interested in the Bayesian most of all)
# plotIC(motif.fit_RUV)
# 
# #visual check of the lowest BIC
# motif.fit_RUV$bic
# 
# #plot the motifs
# plotMotif(motif.fit_RUV)
# 
# #plot the probability legend
# myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))
# 
# plot.new()
# legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

##RUVs Cormotif log2 of Norm Counts

# lognormcounts_CMF_rep <- as.matrix(set1$normalizedCounts)
# lognormcounts_CMF <- log2(lognormcounts_CMF_rep + 1)
# #add a pseudocount to ensure any values are not negative or zero
# 
# #first want to cut out the replicate samples as not needed for Cormotif
# lognormcounts_CMF <- as.data.frame(lognormcounts_CMF) %>% 
#   dplyr::select(-(contains("6R"))) %>% 
#   as.matrix()
# 
# #14319 genes in 36 columns, set up for plugging into Cormotif
# 
# #now I need to set up my groupid and compid accordingly
# 
# #put together my group id and comparison id to make the correct comparisons between experimental conditions
# 
# #groupid tells which experimental conditions are grouped together
# #compid tells which experimental conditions should be compared against one another
# ##ie DOX24T vs DMSO24T matched control
# 
# groupid_other <- readRDS("data/new/RUV/groupid_other_unrearranged.RDS")
# 
# #now put together your compid
# compid1 <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))

###Run Cormotif log2 normalized counts RUVs

#set the seed the same as the previous one to ensure consistency

#fit Cormotif model
# set.seed(19191)
#only set the seed ONCE

# motif.fit_RUV_log2 <- cormotiffit(
#   exprs = lognormcounts_CMF,
#   groupid = groupid_other,
#   compid = compid1,
#   K = 1:8,
#   max.iter = 500,
#   BIC = TRUE,
#   runtype = "logCPM"
# )

#Warning: Zero sample variances detected, have been offset away from zero#

# saveRDS(motif.fit_RUV_log2, "data/new/RUV/motif.fit_RUVnormcounts_log2NC_250629.RDS")
# motif.fit_RUV_log2 <- readRDS("data/new/RUV/motif.fit_RUVnormcounts_log2NC_250629.RDS")

###Plot RUVs Cormotif log2norm counts

# #plot the AIC and BIC (we're interested in the Bayesian most of all)
# plotIC(motif.fit_RUV_log2)
# 
# #visual check of the lowest BIC
# motif.fit_RUV_log2$bic
# 
# #plot the motifs
# plotMotif(motif.fit_RUV_log2, title = "Log2 RUVs Norm Counts")
# 
#plot the probability legend
myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "RUVs Plot Cormotif log2 of normcounts-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

##Cormotif Log2cpm of Normalized Counts RUVs

#since both the TMM normalized norm counts and the cpm norm counts are giving me issues:
#I am going to try this with just the log2 of the normalized counts from RUVs

lognormcounts_CMF_rep <- as.matrix(set1$normalizedCounts)
lognormcounts_CMF_cpm <- cpm(lognormcounts_CMF_rep + 1, log = TRUE)
#add a pseudocount to ensure any values are not negative or zero

#first want to cut out the replicate samples as not needed for Cormotif
lognormcounts_CMF_cpm <- as.data.frame(lognormcounts_CMF_cpm) %>% 
  dplyr::select(-(contains("6R"))) %>% 
  as.matrix()
#14319 genes in 36 cols

#write.csv(x = logNC_CMF_RUV, file = "data/new/RUV/Cormotif_log2normcounts_RUV_matrix.csv")

#14319 genes in 36 columns, set up for plugging into Cormotif

#now I need to set up my groupid and compid accordingly

#put together my group id and comparison id to make the correct comparisons between experimental conditions

#groupid tells which experimental conditions are grouped together
#compid tells which experimental conditions should be compared against one another
##ie DOX24T vs DMSO24T matched control

groupid_other <- readRDS("data/new/RUV/groupid_other_unrearranged.RDS")

#now I have to make this into a vector (named vector)?

compid <- data.frame(Cond1 = c(1, 3, 5), Cond2 = c(2, 4, 6))
compid1 <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))

###Run Cormotif log2cpm Norm Counts RUVs

#set the seed the same as the previous one to ensure consistency

#fit Cormotif model
# set.seed(19191)
#only set the seed ONCE

# motif.fit_RUV_logNC <- cormotiffit(
#   exprs = lognormcounts_CMF_cpm,
#   groupid = groupid_other,
#   compid = compid1,
#   K = 1:8,
#   max.iter = 500,
#   BIC = TRUE,
#   runtype = "logCPM"
# )

# saveRDS(motif.fit_RUV_logNC, "data/new/RUV/motif.fit_RUVnormcounts_log2cpm_250630.RDS")
motif.fit_RUV_logNC_cpm <- readRDS("data/new/RUV/motif.fit_RUVnormcounts_log2cpm_250630.RDS")

###Plot Cormotif log2cpm Norm Counts RUVs

#plot the AIC and BIC (we're interested in the Bayesian most of all)
plotIC(motif.fit_RUV_logNC_cpm)

Past versions of "RUVs Plot Cormotif log2cpm normcounts-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#visual check of the lowest BIC
motif.fit_RUV_logNC_cpm$bic

     K      bic
[1,] 1 167129.9
[2,] 2 166504.4
[3,] 3 166544.8
[4,] 4 166585.1
[5,] 5 166628.6
[6,] 6 166669.3
[7,] 7 166709.8
[8,] 8 166751.7

#plot the motifs
plotMotif(motif.fit_RUV_logNC_cpm)

Past versions of "RUVs Plot Cormotif log2cpm normcounts-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#plot the probability legend
myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "RUVs Plot Cormotif log2cpm normcounts-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

#Log2cpm Norm Counts Cormotif Downstream Analysis

#extract the posterior probability that these DEGs belong to motifs
gene_prob_all_RUV <- motif.fit_RUV_logNC_cpm$bestmotif$p.post
rownames(gene_prob_all_RUV) <- rownames(lognormcounts_CMF_cpm)

#assign each gene to a motif with max post prob
assigned_motifs_RUV <- apply(gene_prob_all_RUV, 1, which.max)
max_probs_RUV <- apply(gene_prob_all_RUV, 1, max)

#combine these into a dataframe - motif assigned genes (p.post)
motif_assignment_df_RUV <- gene_prob_all_RUV %>%
  as.data.frame() %>%
  rownames_to_column("Gene") %>%
  mutate(
    Assigned_Motif = assigned_motifs_RUV[Gene],
    Max_Probability = max_probs_RUV[Gene]
  )

#make some histograms of the unfiltered data from Cormotif p.post

gene_prob_all_RUV %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V1))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes p.post RUV M1")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Cormotif log2cpm Norm Counts clustlike + p.post-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

gene_prob_all_RUV %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V2))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes p.post RUV M2")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Cormotif log2cpm Norm Counts clustlike + p.post-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#extract the cluster likelihood - which DEGs are most likely to be in this cluster
motif_prob_RUV <- motif.fit_RUV_logNC_cpm$bestmotif$clustlike
rownames(motif_prob_RUV) <- rownames(gene_prob_all_RUV)
# write.csv(motif_prob_RUV,"data/new/cormotif_probability_genelist_all_RUV_log2cpm_NormCounts.csv")

#make some histograms to look at the distribution of clustlike genes without filtering
motif_prob_RUV %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V1))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes clustlike Distribution M1")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Cormotif log2cpm Norm Counts clustlike + p.post-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

motif_prob_RUV %>% 
  as.data.frame() %>% 
  ggplot(., aes(x = V2))+
  geom_histogram(bins = 50)+
  xlim(0,1)+
  ggtitle("Cormotif Genes clustlike Distribution M2")

Warning: Removed 2 rows containing missing values or values outside the scale range
(`geom_bar()`).

Past versions of "Cormotif log2cpm Norm Counts clustlike + p.post-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

##P.post and Clustlike Together log2cpm norm counts Cormotif RUV

#begin with the clustlike cutoffs and then overlay the p.post to check if the genes are present in both

#these filters are the combination of the above analysis to get a gene set that fits in both p.post and clustlike

####motif 1####
#filter 1: clustlike
clust1_genes_RUV <- 
  motif_prob_RUV %>%
  as.data.frame() %>%
  filter(V1>0.8 & V2<0.5) %>% 
  rownames
length(clust1_genes_RUV)

[1] 13600

#13600 genes

### Filter 2: Gene-level posterior pattern
prob_filtered_genes_1_RUV <- rownames(gene_prob_all_RUV[(gene_prob_all_RUV[,1] >0.05 & gene_prob_all_RUV[,1] <0.5 & gene_prob_all_RUV[,2] <0.5 & gene_prob_all_RUV[,3] <0.5),])
### Final intersection of both filters
final_genes_1_RUV <- intersect(clust1_genes_RUV, prob_filtered_genes_1_RUV)
cat("Number of genes passing both filters:", length(final_genes_1_RUV), "\n")

Number of genes passing both filters: 7602 

#7602 genes pass both filters here

####motif 2####
#filter 1: clustlike
clust2_genes_RUV <- motif_prob_RUV %>%
  as.data.frame() %>%
  filter(V2>0.5 & V1<0.5) %>% 
  rownames

length(clust2_genes_RUV)

[1] 517

#517 genes

### Filter 2: Gene-level posterior pattern
prob_filtered_genes_2_RUV <- rownames(gene_prob_all_RUV[(gene_prob_all_RUV[,1] >0.3 & gene_prob_all_RUV[,2] >0.5 & gene_prob_all_RUV[,3] >0.5),])
### Final intersection of both filters
final_genes_2_RUV <- intersect(clust2_genes_RUV, prob_filtered_genes_2_RUV)
cat("Number of genes passing both filters:", length(final_genes_2_RUV), "\n")

Number of genes passing both filters: 501 

#501 genes pass both filters here

#what is the proportion of my genes that are included?
#p.post and clustlike together
7673+501

[1] 8174

#8174
(8174/14319)*100

[1] 57.08499

#57.08% of my genes are represented here out of the 14319 original

#what is the proportion of my genes that are included?
#clustlike only
13600+517

[1] 14117

#14117
(14117/14319)*100

[1] 98.58929

#98.6% of my genes are included with clustlike only
#want to find out which genes are not assigned to motifs

final_genes_list_RUV <- union(final_genes_1_RUV, final_genes_2_RUV)
length(final_genes_list_RUV)

[1] 8103

#8174 genes as found above
initial_genes_list_RUV <- rownames(lognormcounts_CMF_cpm)
length(initial_genes_list_RUV)

[1] 14319

#14319 genes as usual

unassigned_genes_list_RUV <- setdiff(initial_genes_list_RUV, final_genes_list_RUV)
length(unassigned_genes_list_RUV)

[1] 6216

#6145 genes not assigned

final_genes_list_clustlike_RUV <- union(clust1_genes_RUV, clust2_genes_RUV)
length(final_genes_list_clustlike_RUV)

[1] 14117

#14117 genes as above with clustlike only

unassigned_genes_list_RUV_clustlike <- setdiff(initial_genes_list_RUV, final_genes_list_clustlike_RUV)
length(unassigned_genes_list_RUV_clustlike)

[1] 202

#202 genes not assigned

# saveRDS(unassigned_genes_list_RUV, "data/new/RUV/CMF/unassigned_genes_RUVlog2cpm_NormCounts_Cormotif.RDS")

# saveRDS(unassigned_genes_list_RUV_clustlike, "data/new/RUV/CMF/unassigned_genes_clustlike_RUVslog2cpm_NormCounts_Cormotif.RDS")

#now, ensure that none of these genes are shared amongst categories
vennCor_final_RUV <- list(final_genes_1_RUV, final_genes_2_RUV)
ggVennDiagram(
  vennCor_final_RUV,
  category.names = c("M1", "M2")
) + ggtitle("Cormotif DEGs clustlike + p.post RUVs log2cpm NC")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Use p.post and clustlike together-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

vennCor_final_RUV_clust <- list(clust1_genes_RUV, clust2_genes_RUV)
ggVennDiagram(
  vennCor_final_RUV_clust,
  category.names = c("M1", "M2")
) + ggtitle("Cormotif DEGs clustlike RUVs log2cpm NC")+
  theme(
    plot.title = element_text(size = 16, face = "bold"),  # Increase title size
    text = element_text(size = 16)  # Increase text size globally
  )

Past versions of "Use p.post and clustlike together-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#no overlapping genes found in these gene sets

clusterdata_dxr_fin_RUV <- data.frame(
  Category = c("Motif 1", "Motif 2"), 
  Value = c(length(final_genes_1_RUV), length(final_genes_2_RUV)
))

clusterdata_dxr_fin_RUV_clust <- data.frame(
  Category = c("Motif 1", "Motif 2"), 
  Value = c(length(clust1_genes_RUV), length(clust2_genes_RUV)
))


piecolors_dxr_fin <- c("Motif 1" = "#007896", 
                       "Motif 2" = "#58508D")

#make a piechart of these distributions
clusterdata_dxr_fin_RUV %>% ggplot(aes(x = "", y = Value, fill = Category))+
  geom_bar(width = 1, stat = "identity")+
  coord_polar("y", start = 0)+
  geom_text(aes(label = Value),
            position = position_stack(vjust = 0.5),
            size = 4, color = "black")+
  labs(title = "Distr of Gene Clusters Cormotif RUVs", x = NULL, y = NULL)+
  theme_void()+
  scale_fill_manual(values = piecolors_dxr_fin)

Past versions of "Use p.post and clustlike together-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

clusterdata_dxr_fin_RUV_clust %>% ggplot(aes(x = "", y = Value, fill = Category))+
  geom_bar(width = 1, stat = "identity")+
  coord_polar("y", start = 0)+
  geom_text(aes(label = Value),
            position = position_stack(vjust = 0.5),
            size = 4, color = "black")+
  labs(title = "Distr of Gene Clusters Cormotif RUVs clustlike", x = NULL, y = NULL)+
  theme_void()+
  scale_fill_manual(values = piecolors_dxr_fin)

Past versions of "Use p.post and clustlike together-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#now, continue by plotting the logFC of all of these gene sets per motif, as well as look at some random genes for log2cpm to see if the patterns are reflected in the example genes

###clustlike RUVs log2cpm Norm Counts RUVs logFC

####clustlike + p.post logFC of initial set####

##motif 1
length(final_genes_1_RUV)

[1] 7602

##motif 2 
length(final_genes_2_RUV)

[1] 501

#Combine the toptables I have from pairwise analysis into a single dataframe
d24_toptable_dxr_RUV <- Toptable_RUV_24T %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24T")

d24r_toptable_dxr_RUV <- Toptable_RUV_24R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "24R")

d144r_toptable_dxr_RUV <- Toptable_RUV_144R %>% 
  rownames_to_column(var = "entrezgene_ID") %>% 
  mutate(Time = "144R")

combined_toptables_dxr_RUV <- bind_rows(
  d24_toptable_dxr_RUV,
  d24r_toptable_dxr_RUV,
  d144r_toptable_dxr_RUV)

#Filter the data based on each motif
filt_toptable_dxr_fin_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_1_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC Motif 1 RUVs clustlike + p.post (n=7673)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_dxr_fin_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC Motif 2 RUVs clustlike + p.post (n=501)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))


#plots
filt_toptable_dxr_fin_RUV

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

filt_toptable_2_dxr_fin_RUV 

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#now plot the abs logFC for each of these too
filt_toptable_abs_fin_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_1_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC Motif 1 RUVs clustlike + p.post (n=7673)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_abs_fin_RUV <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_2_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC Motif 2 RUVs clustlike + p.post (n=501)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_3_abs_fin <- combined_toptables_dxr %>% 
  dplyr::filter(entrezgene_ID  %in% final_genes_3) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC for all genes in Motif 3 (n=231)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#plots
filt_toptable_abs_fin_RUV

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

filt_toptable_2_abs_fin_RUV

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

####Now do this but have it for the clustlike only genes
##motif 1
length(clust1_genes_RUV)

[1] 13600

#13600
##motif 2 
length(clust2_genes_RUV)

[1] 517

#517 genes

#Filter the data based on each motif
filt_toptable_dxr_fin_RUV_clust <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% clust1_genes_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC Motif 1 RUVs clustlike (n=13600)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_dxr_fin_RUV_clust <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% clust2_genes_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = logFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("logFC")+
  theme_bw()+
  ggtitle("LogFC Motif 2 RUVs clustlike (n=517)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))


#plots
filt_toptable_dxr_fin_RUV_clust

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-5.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

filt_toptable_2_dxr_fin_RUV_clust

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#now plot the abs logFC for each of these too
filt_toptable_abs_fin_RUV_clust <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% clust1_genes_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC Motif 1 RUVs clustlike (n=13600)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))

#motif 2
filt_toptable_2_abs_fin_RUV_clust <- combined_toptables_dxr_RUV %>% 
  dplyr::filter(entrezgene_ID  %in% clust2_genes_RUV) %>% 
  mutate(absFC = abs(logFC)) %>% 
  mutate(time = factor(Time, levels = c("24T", "24R", "144R"), labels = c("24hr", "24hr Recovery", "144hr Recovery"))) %>% 
  ggplot(., aes(x = time, y = absFC))+
  geom_boxplot(aes(fill = time))+
  scale_fill_manual(values = time_col)+
  guides(fill = guide_legend(title = "Time"))+
  theme_bw()+
  xlab(" ")+
  ylab("|logFC|")+
  theme_bw()+
  ggtitle("Abs LogFC Motif 2 RUVs clustlike (n=517)")+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        strip.background = element_rect(fill = "#CAD899"),
        axis.text.x = element_text(size = 8, colour = "white", angle = 15),
        strip.text.x = element_text(size = 12, colour = "black", face = "bold"))


#plots
filt_toptable_abs_fin_RUV_clust

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-7.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

filt_toptable_2_abs_fin_RUV_clust

Past versions of "Cormotif log2cpm Norm Counts RUVs Plot logFC-8.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

###log2cpm Example Genes Cormotif RUVs log2cpm Norm Counts

#use the final genes from cross-verifying with clustlike + p.post

#Load in my count matrices
#final_genes_1_RUV
#final_genes_2_RUV

#clust1_genes_RUV
#clust2_genes_RUV

#these are all the genes that are present in each category, make them into dataframes by filtering out the rest of the genes in my main boxplot df
boxplots_cormotif <- boxplot1

motif1_genes_fin_RUV <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% final_genes_1_RUV,]
dim(motif1_genes_fin_RUV)

[1] 7602   44

#7602 genes in 44 cols
motif2_genes_fin_RUV <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% final_genes_2_RUV,]
dim(motif2_genes_fin_RUV)

[1] 501  44

#501 genes in 44 cols

#pull out some random genes for each using sample

m1_genes_fin_RUV <- motif1_genes_fin_RUV[sample(nrow(motif1_genes_fin_RUV), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes1_fin_RUV <- c(m1_genes_fin_RUV$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_data_1_fin_RUV <- function(gene) {
  gene_data <- m1_genes_fin_RUV %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes1_fin_RUV) {
  gene_data <- process_gene_data_1_fin_RUV(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression", gene, "Motif 1 RUVs")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#####motif 2#####

m2_genes_fin_RUV <- motif2_genes_fin_RUV[sample(nrow(motif2_genes_fin_RUV), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes2_fin_RUV <- c(m2_genes_fin_RUV$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_datam2_fin_RUV <- function(gene) {
  gene_data <- motif2_genes_fin_RUV %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#this function is saved under process_gene_data so I will save as an R object

#saveRDS(process_gene_data, "data/new/process_gene_data_funct.RDS")

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes2_fin_RUV) {
  gene_data <- process_gene_datam2_fin_RUV(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression", gene, "Motif 2 RUVs")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-5.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif log2cpm Norm Counts-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

##log2cpm Example Genes Cormotif clustlike

#use the final genes from cross-verifying with clustlike + p.post

#Load in my count matrices

#clust1_genes_RUV
#clust2_genes_RUV

#these are all the genes that are present in each category, make them into dataframes by filtering out the rest of the genes in my main boxplot df
boxplots_cormotif <- boxplot1

motif1_genes_fin_RUV_clust <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% clust1_genes_RUV,]
dim(motif1_genes_fin_RUV_clust)

[1] 13600    44

#13600 genes in 44 cols
motif2_genes_fin_RUV_clust <- boxplots_cormotif[boxplots_cormotif$Entrez_ID %in% clust2_genes_RUV,]
dim(motif2_genes_fin_RUV_clust)

[1] 517  44

#517 genes in 44 cols

#pull out some random genes for each using sample

m1_genes_fin_RUV_clust <- motif1_genes_fin_RUV_clust[sample(nrow(motif1_genes_fin_RUV_clust), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes1_fin_RUV_clust <- c(m1_genes_fin_RUV_clust$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_data_1_fin_RUV_clust <- function(gene) {
  gene_data <- m1_genes_fin_RUV_clust %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes1_fin_RUV_clust) {
  gene_data <- process_gene_data_1_fin_RUV_clust(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression", gene, "M1 RUVs clustlike")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#####motif 2#####

m2_genes_fin_RUV_clust <- motif2_genes_fin_RUV_clust[sample(nrow(motif2_genes_fin_RUV_clust), 3), , drop = FALSE]

#Define gene list(s)
#these are the genes pulled out by m1_genes
initial_test_genes2_fin_RUV_clust <- c(m2_genes_fin_RUV_clust$SYMBOL)  
#Add more gene symbols as needed or add more categories

#Now put in the function I want to use to generate boxplots of genes
process_gene_datam2_fin_RUV_clust <- function(gene) {
  gene_data <- motif2_genes_fin_RUV_clust %>% filter(SYMBOL == gene)
  long_data <- gene_data %>%
    pivot_longer(cols = -c(Entrez_ID, SYMBOL), names_to = "Sample", values_to = "log2CPM") %>%
    mutate(
      Drug = case_when(
        grepl("DOX", Sample) ~ "DOX",
        grepl("DMSO", Sample) ~ "DMSO",
        TRUE ~ NA_character_
      ),
      Timepoint = case_when(
        grepl("_24T_", Sample) ~ "24T",
        grepl("_24R_", Sample) ~ "24R",
        grepl("_144R_", Sample) ~ "144R",
        TRUE ~ NA_character_
      ),
      Indv = case_when(
        grepl("Ind1$", Sample) ~ "1",
        grepl("Ind2$", Sample) ~ "2",
        grepl("Ind3$", Sample) ~ "3",
        grepl("Ind4$", Sample) ~ "4",
        grepl("Ind5$", Sample) ~ "5",
        grepl("Ind6$", Sample) ~ "6",
        grepl("Ind6REP$", Sample) ~ "6R",
        TRUE ~ NA_character_
      ),
      Condition = paste(Drug, Timepoint, sep = "_")
    )
  long_data$Condition <- factor(
    long_data$Condition,
    levels = c(
      "DOX_24T", 
      "DMSO_24T", 
      "DOX_24R", 
      "DMSO_24R", 
      "DOX_144R", 
      "DMSO_144R"
    )
  )
  return(long_data)
}

#this function is saved under process_gene_data so I will save as an R object

#saveRDS(process_gene_data, "data/new/process_gene_data_funct.RDS")

#Generate Boxplots from the above function using our gene list above
for (gene in initial_test_genes2_fin_RUV_clust) {
  gene_data <- process_gene_datam2_fin_RUV_clust(gene)
  p <- ggplot(gene_data, aes(x = Condition, y = log2CPM, fill = Drug)) +
    geom_boxplot(outlier.shape = NA) +
    geom_point(aes(color = Indv), size = 2, alpha = 0.5, position = position_jitter(width = -1, height = 0)) +
    scale_fill_manual(values = c("DOX" = "#499FBD", "DMSO" = "#BBBBBC")) +
    ggtitle(paste("Log2CPM Expression", gene, "M2 RUVs clustlike")) +
    labs(x = "Treatment", y = "log2CPM") +
    theme_bw() +
    theme(
      plot.title = element_text(size = rel(2), hjust = 0.5),
      axis.title = element_text(size = 15, color = "black"),
      axis.text.x = element_text(size = 10, color = "black", angle = 90, hjust = 1)
    )
  print(p)
}

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-4.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-5.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

Past versions of "log2cpm Example Genes Cormotif RUVs clustlike-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

###Cormotif RUVs log2cpm Norm Counts GO/KEGG

#now take these final gene sets for each motif - clustlike + p.post consensus genes

# final_genes_1_RUV
# final_genes_2_RUV

#clust1_genes_RUV
#clust2_genes_RUV


library(gprofiler2)
#####Motif 1 Gene Set#####
# motif1_genes_matrix_RUV <- as.matrix(final_genes_1_RUV) 
# colnames(motif1_genes_matrix_RUV) <- c("entrezgene_ID")

# saveRDS(motif1_genes_matrix_RUV, "data/new/RUV/CMF/motif1_genes_matrix_RUV.RDS")

motif1_genes_matrix_RUV <- readRDS("data/new/RUV/CMF/motif1_genes_matrix_RUV.RDS")
length(motif1_genes_matrix_RUV)

[1] 7602

#7602 genes in this set for motif 1

motif1_mat_GOKEGG_RUV <- gost(query = motif1_genes_matrix_RUV,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif1_GOKEGG_genes_RUV <- gostplot(motif1_mat_GOKEGG_RUV, capped = FALSE, interactive = TRUE)
motif1_GOKEGG_genes_RUV

table_motif1_GOKEGG_genes_RUV <- motif1_mat_GOKEGG_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif1_GOKEGG_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0019538	protein metabolic process	2065	4721	4.931e-103
GO:BP	GO:0080090	regulation of primary metabolic process	2228	5390	7.135e-83
GO:BP	GO:0006996	organelle organization	1583	3594	3.383e-76
GO:BP	GO:0046907	intracellular transport	747	1381	5.019e-76
GO:BP	GO:0051179	localization	2247	5555	3.318e-73
GO:BP	GO:0051641	cellular localization	1585	3661	7.452e-70
GO:BP	GO:0006810	transport	1830	4407	8.187e-66
GO:BP	GO:0051649	establishment of localization in cell	966	2010	1.457e-64
GO:BP	GO:0043412	macromolecule modification	1339	3030	1.398e-63
GO:BP	GO:0048518	positive regulation of biological process	2439	6264	9.096e-63
GO:BP	GO:0048522	positive regulation of cellular process	2324	5920	2.497e-62
GO:BP	GO:0036211	protein modification process	1263	2846	1.005e-60
GO:BP	GO:0009056	catabolic process	1179	2639	5.706e-58
GO:BP	GO:0008104	protein localization	1223	2770	5.624e-57
GO:BP	GO:0070727	cellular macromolecule localization	1227	2782	6.554e-57
GO:BP	GO:0033036	macromolecule localization	1385	3228	1.242e-56
GO:BP	GO:0009057	macromolecule catabolic process	712	1417	1.769e-55
GO:BP	GO:0065007	biological regulation	4404	12743	4.108e-55
GO:BP	GO:0051234	establishment of localization	1960	4928	2.259e-54
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	1631	3990	1.070e-51
GO:BP	GO:0071705	nitrogen compound transport	895	1923	1.070e-51
GO:BP	GO:0015031	protein transport	711	1444	3.658e-51
GO:BP	GO:0033554	cellular response to stress	856	1830	2.332e-50
GO:BP	GO:0035556	intracellular signal transduction	1268	2965	3.801e-50
GO:BP	GO:0023051	regulation of signaling	1445	3478	2.022e-49
GO:BP	GO:0009966	regulation of signal transduction	1287	3034	1.001e-48
GO:BP	GO:0050789	regulation of biological process	4250	12336	4.563e-48
GO:BP	GO:0010646	regulation of cell communication	1441	3486	9.475e-48
GO:BP	GO:0051252	regulation of RNA metabolic process	1506	3687	1.105e-46
GO:BP	GO:0050794	regulation of cellular process	4125	11946	3.132e-46
GO:BP	GO:0030163	protein catabolic process	531	1030	8.599e-45
GO:BP	GO:0048583	regulation of response to stimulus	1595	3993	4.592e-43
GO:BP	GO:0019222	regulation of metabolic process	2593	7035	8.796e-43
GO:BP	GO:0006351	DNA-templated transcription	1432	3549	1.977e-40
GO:BP	GO:2001141	regulation of RNA biosynthetic process	1385	3428	3.584e-39
GO:BP	GO:0006355	regulation of DNA-templated transcription	1378	3409	4.491e-39
GO:BP	GO:0051246	regulation of protein metabolic process	827	1855	1.476e-38
GO:BP	GO:0009893	positive regulation of metabolic process	1436	3597	1.131e-37
GO:BP	GO:0032446	protein modification by small protein conjugation	441	853	3.256e-37
GO:BP	GO:0045184	establishment of protein localization	852	1937	3.512e-37
GO:BP	GO:0032502	developmental process	2402	6553	4.791e-36
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	486	975	7.565e-36
GO:BP	GO:0043687	post-translational protein modification	506	1027	1.037e-35
GO:BP	GO:0007275	multicellular organism development	1805	4727	1.310e-35
GO:BP	GO:0016192	vesicle-mediated transport	719	1592	2.561e-35
GO:BP	GO:0006796	phosphate-containing compound metabolic process	1012	2407	4.839e-35
GO:BP	GO:0006793	phosphorus metabolic process	1013	2410	4.903e-35
GO:BP	GO:1902531	regulation of intracellular signal transduction	849	1953	8.054e-35
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	407	786	1.798e-34
GO:BP	GO:0051128	regulation of cellular component organization	1014	2433	2.619e-33
GO:BP	GO:0006886	intracellular protein transport	363	686	4.260e-33
GO:BP	GO:0016567	protein ubiquitination	396	768	5.554e-33
GO:BP	GO:0009894	regulation of catabolic process	503	1040	6.446e-33
GO:BP	GO:0048856	anatomical structure development	2204	5997	9.061e-33
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	1303	3288	7.825e-32
GO:BP	GO:0060255	regulation of macromolecule metabolic process	2354	6492	3.103e-31
GO:BP	GO:0061919	process utilizing autophagic mechanism	321	597	7.677e-31
GO:BP	GO:0006914	autophagy	321	597	7.677e-31
GO:BP	GO:0048731	system development	1552	4053	4.097e-30
GO:BP	GO:0006366	transcription by RNA polymerase II	1086	2711	9.422e-28
GO:BP	GO:0007005	mitochondrion organization	246	435	1.022e-27
GO:BP	GO:0009968	negative regulation of signal transduction	594	1326	1.318e-27
GO:BP	GO:0048585	negative regulation of response to stimulus	723	1680	1.327e-27
GO:BP	GO:0006412	translation	365	727	2.283e-27
GO:BP	GO:0141124	intracellular signaling cassette	802	1912	1.228e-26
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	845	2036	1.915e-26
GO:BP	GO:0010498	proteasomal protein catabolic process	288	543	2.843e-26
GO:BP	GO:0023057	negative regulation of signaling	629	1435	3.007e-26
GO:BP	GO:0010648	negative regulation of cell communication	629	1436	3.722e-26
GO:BP	GO:0019941	modification-dependent protein catabolic process	326	638	4.619e-26
GO:BP	GO:0002181	cytoplasmic translation	119	165	4.898e-26
GO:BP	GO:0006950	response to stress	1493	3948	9.167e-26
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	327	643	1.090e-25
GO:BP	GO:0048519	negative regulation of biological process	2108	5834	1.108e-25
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	1029	2578	1.767e-25
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	320	628	2.548e-25
GO:BP	GO:0006915	apoptotic process	800	1923	2.636e-25
GO:BP	GO:0016236	macroautophagy	209	362	4.216e-25
GO:BP	GO:0051716	cellular response to stimulus	2593	7376	6.940e-25
GO:BP	GO:0048523	negative regulation of cellular process	2036	5629	8.969e-25
GO:BP	GO:0008219	cell death	821	1991	1.215e-24
GO:BP	GO:0012501	programmed cell death	819	1987	1.640e-24
GO:BP	GO:0007399	nervous system development	1033	2604	1.664e-24
GO:BP	GO:0048193	Golgi vesicle transport	184	312	1.567e-23
GO:BP	GO:0051248	negative regulation of protein metabolic process	334	677	2.492e-23
GO:BP	GO:0065008	regulation of biological quality	1140	2947	1.300e-22
GO:BP	GO:0033365	protein localization to organelle	531	1209	3.643e-22
GO:BP	GO:0006508	proteolysis	631	1486	4.204e-22
GO:BP	GO:0044238	primary metabolic process	4092	12342	9.259e-22
GO:BP	GO:0060341	regulation of cellular localization	457	1013	1.063e-21
GO:BP	GO:0044087	regulation of cellular component biogenesis	456	1011	1.248e-21
GO:BP	GO:0032879	regulation of localization	820	2029	1.518e-21
GO:BP	GO:0033043	regulation of organelle organization	506	1148	1.791e-21
GO:BP	GO:0051130	positive regulation of cellular component organization	489	1105	3.794e-21
GO:BP	GO:0051253	negative regulation of RNA metabolic process	596	1400	4.107e-21
GO:BP	GO:0051254	positive regulation of RNA metabolic process	750	1835	4.531e-21
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	641	1529	7.494e-21
GO:BP	GO:0080135	regulation of cellular response to stress	263	519	2.842e-20
GO:BP	GO:0009889	regulation of biosynthetic process	2061	5809	4.830e-20
GO:BP	GO:0007010	cytoskeleton organization	637	1529	6.275e-20
GO:BP	GO:0009891	positive regulation of biosynthetic process	1039	2696	1.028e-19
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	656	1588	1.652e-19
GO:BP	GO:0030030	cell projection organization	671	1631	1.778e-19
GO:BP	GO:0032880	regulation of protein localization	409	907	2.724e-19
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	316	662	3.332e-19
GO:BP	GO:0065009	regulation of molecular function	622	1496	3.408e-19
GO:BP	GO:0034504	protein localization to nucleus	177	318	7.132e-19
GO:BP	GO:0097190	apoptotic signaling pathway	293	606	9.092e-19
GO:BP	GO:0006974	DNA damage response	407	908	1.236e-18
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	997	2593	1.837e-18
GO:BP	GO:0016310	phosphorylation	556	1320	1.980e-18
GO:BP	GO:0070925	organelle assembly	456	1046	3.656e-18
GO:BP	GO:0031399	regulation of protein modification process	457	1049	3.837e-18
GO:BP	GO:0050793	regulation of developmental process	949	2457	3.969e-18
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	546	1296	4.158e-18
GO:BP	GO:0050896	response to stimulus	3046	8999	4.729e-18
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	540	1280	4.756e-18
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	687	1699	7.636e-18
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	1991	5644	8.673e-18
GO:BP	GO:0030029	actin filament-based process	373	825	8.673e-18
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	686	1697	8.673e-18
GO:BP	GO:0034976	response to endoplasmic reticulum stress	154	270	9.307e-18
GO:BP	GO:0071495	cellular response to endogenous stimulus	518	1223	1.080e-17
GO:BP	GO:0061024	membrane organization	371	821	1.186e-17
GO:BP	GO:0030036	actin cytoskeleton organization	336	729	1.629e-17
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	185	345	1.893e-17
GO:BP	GO:0010506	regulation of autophagy	194	367	2.037e-17
GO:BP	GO:0006913	nucleocytoplasmic transport	180	334	2.842e-17
GO:BP	GO:0051169	nuclear transport	180	334	2.842e-17
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	126	209	3.641e-17
GO:BP	GO:0006468	protein phosphorylation	517	1227	3.872e-17
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	424	970	4.017e-17
GO:BP	GO:0009967	positive regulation of signal transduction	641	1578	4.111e-17
GO:BP	GO:0009653	anatomical structure morphogenesis	1029	2713	4.342e-17
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	211	414	1.327e-16
GO:BP	GO:0016197	endosomal transport	160	290	1.335e-16
GO:BP	GO:0048584	positive regulation of response to stimulus	896	2331	2.253e-16
GO:BP	GO:0023056	positive regulation of signaling	713	1796	2.342e-16
GO:BP	GO:0090407	organophosphate biosynthetic process	290	619	3.047e-16
GO:BP	GO:0042981	regulation of apoptotic process	596	1462	3.271e-16
GO:BP	GO:0043067	regulation of programmed cell death	611	1506	3.992e-16
GO:BP	GO:0009719	response to endogenous stimulus	605	1489	4.055e-16
GO:BP	GO:0010468	regulation of gene expression	1943	5536	4.090e-16
GO:BP	GO:0030154	cell differentiation	1589	4437	5.139e-16
GO:BP	GO:0007049	cell cycle	665	1663	5.436e-16
GO:BP	GO:0048869	cellular developmental process	1589	4438	5.606e-16
GO:BP	GO:0044281	small molecule metabolic process	704	1776	5.638e-16
GO:BP	GO:0048468	cell development	1075	2876	9.562e-16
GO:BP	GO:0010256	endomembrane system organization	286	613	9.749e-16
GO:BP	GO:0022008	neurogenesis	701	1771	9.749e-16
GO:BP	GO:0006979	response to oxidative stress	203	400	9.749e-16
GO:BP	GO:0023052	signaling	2248	6515	1.874e-15
GO:BP	GO:0006417	regulation of translation	194	380	2.270e-15
GO:BP	GO:0097435	supramolecular fiber organization	377	861	2.546e-15
GO:BP	GO:0010647	positive regulation of cell communication	707	1795	2.571e-15
GO:BP	GO:0051247	positive regulation of protein metabolic process	441	1039	3.583e-15
GO:BP	GO:0019637	organophosphate metabolic process	454	1077	5.072e-15
GO:BP	GO:0007154	cell communication	2250	6540	8.804e-15
GO:BP	GO:0071363	cellular response to growth factor stimulus	311	689	1.128e-14
GO:BP	GO:0016241	regulation of macroautophagy	110	184	1.231e-14
GO:BP	GO:0042254	ribosome biogenesis	169	323	1.231e-14
GO:BP	GO:0070848	response to growth factor	322	721	1.997e-14
GO:BP	GO:0062197	cellular response to chemical stress	166	317	2.023e-14
GO:BP	GO:0071840	cellular component organization or biogenesis	2825	8393	2.339e-14
GO:BP	GO:0071559	response to transforming growth factor beta	146	269	2.339e-14
GO:BP	GO:0009987	cellular process	6272	20247	2.662e-14
GO:BP	GO:0031647	regulation of protein stability	173	335	2.673e-14
GO:BP	GO:0048513	animal organ development	1134	3085	3.100e-14
GO:BP	GO:0080134	regulation of response to stress	559	1387	4.734e-14
GO:BP	GO:1901135	carbohydrate derivative metabolic process	416	983	4.797e-14
GO:BP	GO:0031344	regulation of cell projection organization	297	658	5.181e-14
GO:BP	GO:0010970	transport along microtubule	106	178	5.949e-14
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	462	1113	5.988e-14
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	142	262	6.603e-14
GO:BP	GO:0006091	generation of precursor metabolites and energy	228	478	8.520e-14
GO:BP	GO:0031175	neuron projection development	429	1023	9.544e-14
GO:BP	GO:1901698	response to nitrogen compound	449	1080	1.127e-13
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	398	938	1.241e-13
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	289	642	1.871e-13
GO:BP	GO:0099111	microtubule-based transport	123	220	2.438e-13
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	131	239	2.549e-13
GO:BP	GO:0000209	protein polyubiquitination	148	280	2.671e-13
GO:BP	GO:0032386	regulation of intracellular transport	142	266	3.302e-13
GO:BP	GO:0009896	positive regulation of catabolic process	252	546	3.433e-13
GO:BP	GO:0051650	establishment of vesicle localization	114	200	3.775e-13
GO:BP	GO:0018193	peptidyl-amino acid modification	304	686	4.215e-13
GO:BP	GO:0051049	regulation of transport	630	1607	4.354e-13
GO:BP	GO:0050790	regulation of catalytic activity	392	928	4.379e-13
GO:BP	GO:0007015	actin filament organization	219	461	4.985e-13
GO:BP	GO:0048666	neuron development	480	1177	5.539e-13
GO:BP	GO:1901873	regulation of post-translational protein modification	132	244	7.420e-13
GO:BP	GO:0044093	positive regulation of molecular function	375	884	8.144e-13
GO:BP	GO:0030182	neuron differentiation	574	1451	1.101e-12
GO:BP	GO:0051648	vesicle localization	121	219	1.218e-12
GO:BP	GO:0035966	response to topologically incorrect protein	94	157	1.388e-12
GO:BP	GO:0043254	regulation of protein-containing complex assembly	202	421	1.554e-12
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	93	155	1.570e-12
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	234	505	1.786e-12
GO:BP	GO:0048699	generation of neurons	602	1536	1.873e-12
GO:BP	GO:0042176	regulation of protein catabolic process	181	369	2.676e-12
GO:BP	GO:0009628	response to abiotic stimulus	465	1144	2.697e-12
GO:BP	GO:0051604	protein maturation	246	539	3.136e-12
GO:BP	GO:0051640	organelle localization	276	620	3.647e-12
GO:BP	GO:0010638	positive regulation of organelle organization	228	492	3.668e-12
GO:BP	GO:0007033	vacuole organization	128	239	4.703e-12
GO:BP	GO:0007165	signal transduction	2054	6002	5.612e-12
GO:BP	GO:0006259	DNA metabolic process	414	1005	6.831e-12
GO:BP	GO:0007264	small GTPase-mediated signal transduction	232	505	6.831e-12
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	265	594	8.360e-12
GO:BP	GO:1903829	positive regulation of protein localization	229	499	1.120e-11
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	114	208	1.315e-11
GO:BP	GO:0070887	cellular response to chemical stimulus	819	2192	1.315e-11
GO:BP	GO:0072659	protein localization to plasma membrane	148	291	1.399e-11
GO:BP	GO:0031346	positive regulation of cell projection organization	174	357	1.582e-11
GO:BP	GO:0034599	cellular response to oxidative stress	130	247	1.582e-11
GO:BP	GO:0009060	aerobic respiration	110	199	1.590e-11
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	293	673	1.590e-11
GO:BP	GO:0007017	microtubule-based process	410	999	1.648e-11
GO:BP	GO:0000278	mitotic cell cycle	372	892	1.648e-11
GO:BP	GO:0006753	nucleoside phosphate metabolic process	283	646	1.667e-11
GO:BP	GO:0032501	multicellular organismal process	2463	7322	1.779e-11
GO:BP	GO:0031396	regulation of protein ubiquitination	109	197	1.824e-11
GO:BP	GO:0009895	negative regulation of catabolic process	175	361	2.372e-11
GO:BP	GO:0000902	cell morphogenesis	408	996	2.558e-11
GO:BP	GO:0051094	positive regulation of developmental process	529	1343	2.637e-11
GO:BP	GO:0006325	chromatin organization	368	884	2.889e-11
GO:BP	GO:0072359	circulatory system development	460	1145	2.926e-11
GO:BP	GO:0006897	endocytosis	305	709	2.926e-11
GO:BP	GO:0045333	cellular respiration	127	242	3.656e-11
GO:BP	GO:0016032	viral process	198	423	4.617e-11
GO:BP	GO:0050821	protein stabilization	119	224	6.437e-11
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	181	380	6.562e-11
GO:BP	GO:0022402	cell cycle process	505	1280	6.648e-11
GO:BP	GO:0043065	positive regulation of apoptotic process	237	528	6.803e-11
GO:BP	GO:0036503	ERAD pathway	69	109	7.681e-11
GO:BP	GO:0007166	cell surface receptor signaling pathway	1021	2819	7.681e-11
GO:BP	GO:0016043	cellular component organization	2724	8184	7.724e-11
GO:BP	GO:0006986	response to unfolded protein	83	140	7.855e-11
GO:BP	GO:0006401	RNA catabolic process	155	315	1.076e-10
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	154	314	1.754e-10
GO:BP	GO:0016055	Wnt signaling pathway	209	458	2.145e-10
GO:BP	GO:0051493	regulation of cytoskeleton organization	231	517	2.230e-10
GO:BP	GO:0141188	nucleic acid catabolic process	165	343	2.245e-10
GO:BP	GO:1901699	cellular response to nitrogen compound	278	645	2.295e-10
GO:BP	GO:0042592	homeostatic process	657	1736	2.649e-10
GO:BP	GO:0070201	regulation of establishment of protein localization	238	537	2.852e-10
GO:BP	GO:0051239	regulation of multicellular organismal process	1061	2956	3.159e-10
GO:BP	GO:1990778	protein localization to cell periphery	173	365	3.228e-10
GO:BP	GO:0043068	positive regulation of programmed cell death	241	546	3.448e-10
GO:BP	GO:0034330	cell junction organization	345	834	3.710e-10
GO:BP	GO:0051129	negative regulation of cellular component organization	297	701	4.568e-10
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	172	364	4.992e-10
GO:BP	GO:0051656	establishment of organelle localization	220	491	4.992e-10
GO:BP	GO:0035295	tube development	438	1101	5.283e-10
GO:BP	GO:0072522	purine-containing compound biosynthetic process	130	257	5.333e-10
GO:BP	GO:0030031	cell projection assembly	264	613	8.415e-10
GO:BP	GO:0006606	protein import into nucleus	92	166	9.478e-10
GO:BP	GO:0006457	protein folding	114	219	9.478e-10
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	151	312	9.496e-10
GO:BP	GO:0016477	cell migration	585	1534	9.654e-10
GO:BP	GO:0098657	import into cell	374	922	9.894e-10
GO:BP	GO:0006839	mitochondrial transport	97	178	9.894e-10
GO:BP	GO:0140694	membraneless organelle assembly	196	430	1.031e-09
GO:BP	GO:0010975	regulation of neuron projection development	202	446	1.033e-09
GO:BP	GO:0051170	import into nucleus	94	171	1.037e-09
GO:BP	GO:0031400	negative regulation of protein modification process	165	349	1.181e-09
GO:BP	GO:0016482	cytosolic transport	81	141	1.246e-09
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	128	255	1.429e-09
GO:BP	GO:0030334	regulation of cell migration	386	960	1.782e-09
GO:BP	GO:0008152	metabolic process	4514	14136	1.831e-09
GO:BP	GO:0016072	rRNA metabolic process	132	266	1.929e-09
GO:BP	GO:1902903	regulation of supramolecular fiber organization	177	383	2.337e-09
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	340	831	2.383e-09
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	68	113	2.720e-09
GO:BP	GO:0006403	RNA localization	105	200	2.831e-09
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	257	600	2.835e-09
GO:BP	GO:0001701	in utero embryonic development	188	413	2.873e-09
GO:BP	GO:0051168	nuclear export	92	169	3.274e-09
GO:BP	GO:2000145	regulation of cell motility	406	1022	3.539e-09
GO:BP	GO:0043069	negative regulation of programmed cell death	365	905	3.806e-09
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	486	1256	4.655e-09
GO:BP	GO:0051336	regulation of hydrolase activity	164	352	5.291e-09
GO:BP	GO:0007163	establishment or maintenance of cell polarity	118	234	5.422e-09
GO:BP	GO:0000226	microtubule cytoskeleton organization	281	670	5.422e-09
GO:BP	GO:0016050	vesicle organization	173	376	5.673e-09
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	80	142	5.786e-09
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	232	535	5.828e-09
GO:BP	GO:0060070	canonical Wnt signaling pathway	148	311	6.334e-09
GO:BP	GO:0032456	endocytic recycling	55	86	6.410e-09
GO:BP	GO:0007507	heart development	257	605	7.361e-09
GO:BP	GO:0006338	chromatin remodeling	300	725	7.367e-09
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	81	145	7.702e-09
GO:BP	GO:0015986	proton motive force-driven ATP synthesis	51	78	8.965e-09
GO:BP	GO:0006754	ATP biosynthetic process	62	102	9.756e-09
GO:BP	GO:0061061	muscle structure development	288	693	9.847e-09
GO:BP	GO:0040012	regulation of locomotion	419	1067	1.009e-08
GO:BP	GO:0030111	regulation of Wnt signaling pathway	155	331	1.012e-08
GO:BP	GO:0009142	nucleoside triphosphate biosynthetic process	73	127	1.012e-08
GO:BP	GO:0006281	DNA repair	262	621	1.082e-08
GO:BP	GO:0072521	purine-containing compound metabolic process	241	563	1.105e-08
GO:BP	GO:0009165	nucleotide biosynthetic process	115	229	1.210e-08
GO:BP	GO:0042325	regulation of phosphorylation	336	830	1.222e-08
GO:BP	GO:0019220	regulation of phosphate metabolic process	380	956	1.240e-08
GO:BP	GO:0044092	negative regulation of molecular function	237	553	1.342e-08
GO:BP	GO:0015931	nucleobase-containing compound transport	118	237	1.390e-08
GO:BP	GO:0032869	cellular response to insulin stimulus	106	207	1.390e-08
GO:BP	GO:0008088	axo-dendritic transport	53	83	1.411e-08
GO:BP	GO:0051174	regulation of phosphorus metabolic process	380	957	1.420e-08
GO:BP	GO:0000422	autophagy of mitochondrion	63	105	1.435e-08
GO:BP	GO:0043066	negative regulation of apoptotic process	351	874	1.449e-08
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	130	268	1.604e-08
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	62	103	1.624e-08
GO:BP	GO:1903311	regulation of mRNA metabolic process	147	312	1.628e-08
GO:BP	GO:0006364	rRNA processing	113	225	1.635e-08
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	264	629	1.635e-08
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	463	1199	1.639e-08
GO:BP	GO:0009790	embryo development	441	1135	1.677e-08
GO:BP	GO:0046390	ribose phosphate biosynthetic process	96	183	1.677e-08
GO:BP	GO:0009201	ribonucleoside triphosphate biosynthetic process	69	119	1.719e-08
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	159	344	1.850e-08
GO:BP	GO:0009260	ribonucleotide biosynthetic process	93	176	1.875e-08
GO:BP	GO:0001932	regulation of protein phosphorylation	317	779	1.880e-08
GO:BP	GO:0070936	protein K48-linked ubiquitination	60	99	2.037e-08
GO:BP	GO:0048858	cell projection morphogenesis	282	681	2.148e-08
GO:BP	GO:0060322	head development	326	806	2.357e-08
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	280	676	2.384e-08
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	76	136	2.423e-08
GO:BP	GO:0031401	positive regulation of protein modification process	266	637	2.468e-08
GO:BP	GO:0000165	MAPK cascade	304	744	2.507e-08
GO:BP	GO:1902115	regulation of organelle assembly	116	234	2.533e-08
GO:BP	GO:0008654	phospholipid biosynthetic process	125	257	2.622e-08
GO:BP	GO:0042274	ribosomal small subunit biogenesis	62	104	2.653e-08
GO:BP	GO:0009725	response to hormone	361	907	2.653e-08
GO:BP	GO:0045595	regulation of cell differentiation	589	1576	2.875e-08
GO:BP	GO:1903047	mitotic cell cycle process	304	745	2.918e-08
GO:BP	GO:0035239	tube morphogenesis	351	879	2.928e-08
GO:BP	GO:0006119	oxidative phosphorylation	80	146	3.011e-08
GO:BP	GO:0007420	brain development	307	754	3.145e-08
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	147	315	3.447e-08
GO:BP	GO:0032970	regulation of actin filament-based process	170	376	3.573e-08
GO:BP	GO:0006164	purine nucleotide biosynthetic process	99	193	4.177e-08
GO:BP	GO:0051726	regulation of cell cycle	422	1087	4.271e-08
GO:BP	GO:0032870	cellular response to hormone stimulus	265	638	4.735e-08
GO:BP	GO:1901701	cellular response to oxygen-containing compound	454	1182	5.177e-08
GO:BP	GO:0007034	vacuolar transport	91	174	5.343e-08
GO:BP	GO:0009892	negative regulation of metabolic process	1176	3375	5.976e-08
GO:BP	GO:0051017	actin filament bundle assembly	85	160	6.748e-08
GO:BP	GO:0043009	chordate embryonic development	276	671	6.759e-08
GO:BP	GO:0048812	neuron projection morphogenesis	272	660	7.064e-08
GO:BP	GO:0001944	vasculature development	308	762	7.124e-08
GO:BP	GO:0030162	regulation of proteolysis	180	406	7.326e-08
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	283	692	8.255e-08
GO:BP	GO:0006402	mRNA catabolic process	125	261	8.255e-08
GO:BP	GO:0061572	actin filament bundle organization	86	163	8.299e-08
GO:BP	GO:0005976	polysaccharide metabolic process	60	102	9.644e-08
GO:BP	GO:0010508	positive regulation of autophagy	85	161	9.758e-08
GO:BP	GO:0009152	purine ribonucleotide biosynthetic process	85	161	9.758e-08
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	115	236	9.984e-08
GO:BP	GO:0051028	mRNA transport	72	130	1.044e-07
GO:BP	GO:0009117	nucleotide metabolic process	211	493	1.205e-07
GO:BP	GO:0009145	purine nucleoside triphosphate biosynthetic process	65	114	1.238e-07
GO:BP	GO:0009100	glycoprotein metabolic process	166	371	1.333e-07
GO:BP	GO:0045017	glycerolipid biosynthetic process	120	250	1.408e-07
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	91	177	1.557e-07
GO:BP	GO:0009411	response to UV	82	155	1.591e-07
GO:BP	GO:0051052	regulation of DNA metabolic process	213	500	1.597e-07
GO:BP	GO:0050658	RNA transport	84	160	1.660e-07
GO:BP	GO:0050657	nucleic acid transport	84	160	1.660e-07
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	68	122	1.938e-07
GO:BP	GO:2000026	regulation of multicellular organismal development	530	1418	1.950e-07
GO:BP	GO:0051301	cell division	269	658	2.031e-07
GO:BP	GO:0051236	establishment of RNA localization	85	163	2.031e-07
GO:BP	GO:0048870	cell motility	655	1793	2.033e-07
GO:BP	GO:0007040	lysosome organization	64	113	2.249e-07
GO:BP	GO:0080171	lytic vacuole organization	64	113	2.249e-07
GO:BP	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	64	113	2.249e-07
GO:BP	GO:0031334	positive regulation of protein-containing complex assembly	100	201	2.550e-07
GO:BP	GO:0007041	lysosomal transport	74	137	2.625e-07
GO:BP	GO:0044042	glucan metabolic process	52	86	2.717e-07
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	151	334	2.722e-07
GO:BP	GO:0000302	response to reactive oxygen species	99	199	3.000e-07
GO:BP	GO:0034614	cellular response to reactive oxygen species	78	147	3.000e-07
GO:BP	GO:0005977	glycogen metabolic process	51	84	3.062e-07
GO:BP	GO:0007020	microtubule nucleation	33	46	3.149e-07
GO:BP	GO:0001568	blood vessel development	294	732	3.183e-07
GO:BP	GO:0000423	mitophagy	45	71	3.354e-07
GO:BP	GO:0043087	regulation of GTPase activity	100	202	3.454e-07
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	98	197	3.504e-07
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	90	177	3.555e-07
GO:BP	GO:0042542	response to hydrogen peroxide	57	98	3.849e-07
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	43	67	4.038e-07
GO:BP	GO:1901700	response to oxygen-containing compound	611	1669	4.621e-07
GO:BP	GO:0099003	vesicle-mediated transport in synapse	121	257	4.651e-07
GO:BP	GO:0007029	endoplasmic reticulum organization	59	103	4.659e-07
GO:BP	GO:0019693	ribose phosphate metabolic process	167	380	5.212e-07
GO:BP	GO:0040007	growth	361	929	5.399e-07
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	128	276	5.539e-07
GO:BP	GO:0007417	central nervous system development	406	1061	5.738e-07
GO:BP	GO:0009888	tissue development	730	2032	5.939e-07
GO:BP	GO:0017148	negative regulation of translation	71	132	6.228e-07
GO:BP	GO:0043603	amide metabolic process	194	455	6.473e-07
GO:BP	GO:1905037	autophagosome organization	68	125	6.714e-07
GO:BP	GO:0018105	peptidyl-serine phosphorylation	88	174	6.894e-07
GO:BP	GO:0000045	autophagosome assembly	65	118	7.091e-07
GO:BP	GO:0008610	lipid biosynthetic process	291	729	7.237e-07
GO:BP	GO:0006282	regulation of DNA repair	108	225	7.344e-07
GO:BP	GO:0033157	regulation of intracellular protein transport	79	152	7.603e-07
GO:BP	GO:0060627	regulation of vesicle-mediated transport	221	531	7.630e-07
GO:BP	GO:0007006	mitochondrial membrane organization	64	116	8.250e-07
GO:BP	GO:0019080	viral gene expression	61	109	8.497e-07
GO:BP	GO:0009259	ribonucleotide metabolic process	163	372	9.451e-07
GO:BP	GO:0043487	regulation of RNA stability	95	193	1.067e-06
GO:BP	GO:0051258	protein polymerization	130	284	1.085e-06
GO:BP	GO:2000142	regulation of DNA-templated transcription initiation	49	82	1.139e-06
GO:BP	GO:0042177	negative regulation of protein catabolic process	64	117	1.262e-06
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	144	322	1.266e-06
GO:BP	GO:0051223	regulation of protein transport	188	442	1.268e-06
GO:BP	GO:0002262	myeloid cell homeostasis	90	181	1.303e-06
GO:BP	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	36	54	1.332e-06
GO:BP	GO:0051338	regulation of transferase activity	208	498	1.369e-06
GO:BP	GO:0070482	response to oxygen levels	152	344	1.386e-06
GO:BP	GO:0040011	locomotion	469	1255	1.392e-06
GO:BP	GO:0043434	response to peptide hormone	187	440	1.454e-06
GO:BP	GO:0010821	regulation of mitochondrion organization	63	115	1.458e-06
GO:BP	GO:0006893	Golgi to plasma membrane transport	42	67	1.493e-06
GO:BP	GO:0030010	establishment of cell polarity	81	159	1.543e-06
GO:BP	GO:0072331	signal transduction by p53 class mediator	83	164	1.549e-06
GO:BP	GO:0070585	protein localization to mitochondrion	70	132	1.556e-06
GO:BP	GO:0061951	establishment of protein localization to plasma membrane	41	65	1.651e-06
GO:BP	GO:0006629	lipid metabolic process	514	1391	1.661e-06
GO:BP	GO:0034101	erythrocyte homeostasis	76	147	1.751e-06
GO:BP	GO:1904951	positive regulation of establishment of protein localization	146	329	1.779e-06
GO:BP	GO:0042255	ribosome assembly	40	63	1.813e-06
GO:BP	GO:0031929	TOR signaling	84	167	1.813e-06
GO:BP	GO:0061077	chaperone-mediated protein folding	45	74	1.844e-06
GO:BP	GO:0060260	regulation of transcription initiation by RNA polymerase II	45	74	1.844e-06
GO:BP	GO:0048872	homeostasis of number of cells	147	332	1.885e-06
GO:BP	GO:0090066	regulation of anatomical structure size	208	500	1.896e-06
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	120	260	1.920e-06
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	138	308	1.973e-06
GO:BP	GO:0072384	organelle transport along microtubule	52	90	1.982e-06
GO:BP	GO:0034644	cellular response to UV	52	90	1.982e-06
GO:BP	GO:0051240	positive regulation of multicellular organismal process	605	1667	2.032e-06
GO:BP	GO:0043085	positive regulation of catalytic activity	227	554	2.080e-06
GO:BP	GO:0048729	tissue morphogenesis	248	614	2.251e-06
GO:BP	GO:0045727	positive regulation of translation	72	138	2.314e-06
GO:BP	GO:0043408	regulation of MAPK cascade	256	637	2.316e-06
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	1089	3157	2.362e-06
GO:BP	GO:0042594	response to starvation	104	219	2.365e-06
GO:BP	GO:2001234	negative regulation of apoptotic signaling pathway	109	232	2.365e-06
GO:BP	GO:0051668	localization within membrane	355	924	2.514e-06
GO:BP	GO:0006900	vesicle budding from membrane	50	86	2.616e-06
GO:BP	GO:0018209	peptidyl-serine modification	91	186	2.670e-06
GO:BP	GO:1900180	regulation of protein localization to nucleus	75	146	2.856e-06
GO:BP	GO:0006163	purine nucleotide metabolic process	182	430	2.872e-06
GO:BP	GO:0032868	response to insulin	123	270	3.144e-06
GO:BP	GO:1990542	mitochondrial transmembrane transport	55	98	3.168e-06
GO:BP	GO:0009150	purine ribonucleotide metabolic process	153	351	3.302e-06
GO:BP	GO:0050808	synapse organization	229	563	3.542e-06
GO:BP	GO:0006413	translational initiation	67	127	3.592e-06
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	119	260	3.633e-06
GO:BP	GO:0048589	developmental growth	264	663	3.638e-06
GO:BP	GO:0009314	response to radiation	184	437	3.734e-06
GO:BP	GO:0009267	cellular response to starvation	87	177	3.792e-06
GO:BP	GO:0099504	synaptic vesicle cycle	104	221	4.043e-06
GO:BP	GO:0035329	hippo signaling	37	58	4.390e-06
GO:BP	GO:0098930	axonal transport	42	69	4.519e-06
GO:BP	GO:0030335	positive regulation of cell migration	227	559	4.585e-06
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	141	320	4.589e-06
GO:BP	GO:0014706	striated muscle tissue development	173	408	4.923e-06
GO:BP	GO:0002009	morphogenesis of an epithelium	207	503	4.960e-06
GO:BP	GO:0034329	cell junction assembly	207	503	4.960e-06
GO:BP	GO:0006898	receptor-mediated endocytosis	120	264	4.980e-06
GO:BP	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	133	299	5.216e-06
GO:BP	GO:0051054	positive regulation of DNA metabolic process	130	291	5.291e-06
GO:BP	GO:0006626	protein targeting to mitochondrion	57	104	5.419e-06
GO:BP	GO:0001666	response to hypoxia	134	302	5.563e-06
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	90	186	5.603e-06
GO:BP	GO:1903321	negative regulation of protein modification by small protein conjugation or removal	51	90	5.703e-06
GO:BP	GO:0043488	regulation of mRNA stability	88	181	5.794e-06
GO:BP	GO:0035967	cellular response to topologically incorrect protein	59	109	5.908e-06
GO:BP	GO:0060395	SMAD protein signal transduction	47	81	6.404e-06
GO:BP	GO:1903828	negative regulation of protein localization	101	215	6.484e-06
GO:BP	GO:0021537	telencephalon development	127	284	6.669e-06
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	99	210	6.856e-06
GO:BP	GO:0008286	insulin receptor signaling pathway	65	124	7.078e-06
GO:BP	GO:0030522	intracellular receptor signaling pathway	161	377	7.278e-06
GO:BP	GO:0051098	regulation of binding	100	213	7.607e-06
GO:BP	GO:0042273	ribosomal large subunit biogenesis	42	70	7.611e-06
GO:BP	GO:0048871	multicellular organismal-level homeostasis	318	825	7.654e-06
GO:BP	GO:0046034	ATP metabolic process	106	229	8.141e-06
GO:BP	GO:1902600	proton transmembrane transport	91	190	8.368e-06
GO:BP	GO:0006112	energy reserve metabolic process	54	98	8.568e-06
GO:BP	GO:0046785	microtubule polymerization	54	98	8.568e-06
GO:BP	GO:0032535	regulation of cellular component size	153	356	8.800e-06
GO:BP	GO:0061013	regulation of mRNA catabolic process	94	198	8.884e-06
GO:BP	GO:0021543	pallium development	94	198	8.884e-06
GO:BP	GO:0019827	stem cell population maintenance	87	180	9.029e-06
GO:BP	GO:0031669	cellular response to nutrient levels	113	248	9.096e-06
GO:BP	GO:0019058	viral life cycle	136	310	9.539e-06
GO:BP	GO:0006903	vesicle targeting	40	66	9.717e-06
GO:BP	GO:2000147	positive regulation of cell motility	235	587	9.893e-06
GO:BP	GO:0051646	mitochondrion localization	34	53	1.055e-05
GO:BP	GO:0018205	peptidyl-lysine modification	71	140	1.055e-05
GO:BP	GO:0060491	regulation of cell projection assembly	96	204	1.098e-05
GO:BP	GO:0140053	mitochondrial gene expression	82	168	1.137e-05
GO:BP	GO:1901874	negative regulation of post-translational protein modification	52	94	1.159e-05
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	64	123	1.180e-05
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	57	106	1.189e-05
GO:BP	GO:2001235	positive regulation of apoptotic signaling pathway	70	138	1.236e-05
GO:BP	GO:0060537	muscle tissue development	179	430	1.236e-05
GO:BP	GO:0006383	transcription by RNA polymerase III	38	62	1.236e-05
GO:BP	GO:0120032	regulation of plasma membrane bounded cell projection assembly	95	202	1.281e-05
GO:BP	GO:0051896	regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	118	263	1.327e-05
GO:BP	GO:0110053	regulation of actin filament organization	118	263	1.327e-05
GO:BP	GO:0022900	electron transport chain	65	126	1.420e-05
GO:BP	GO:2000144	positive regulation of DNA-templated transcription initiation	41	69	1.434e-05
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	30	45	1.435e-05
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	114	253	1.561e-05
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	80	164	1.565e-05
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	134	307	1.565e-05
GO:BP	GO:0045048	protein insertion into ER membrane	24	33	1.659e-05
GO:BP	GO:0019725	cellular homeostasis	319	835	1.784e-05
GO:BP	GO:0051345	positive regulation of hydrolase activity	96	206	1.839e-05
GO:BP	GO:0036293	response to decreased oxygen levels	137	316	1.853e-05
GO:BP	GO:0040017	positive regulation of locomotion	239	603	1.887e-05
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	105	230	1.958e-05
GO:BP	GO:0048514	blood vessel morphogenesis	250	635	1.973e-05
GO:BP	GO:0055085	transmembrane transport	567	1578	1.977e-05
GO:BP	GO:0045786	negative regulation of cell cycle	159	377	1.988e-05
GO:BP	GO:1901875	positive regulation of post-translational protein modification	67	132	2.001e-05
GO:BP	GO:0045732	positive regulation of protein catabolic process	97	209	2.001e-05
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	82	170	2.001e-05
GO:BP	GO:0032981	mitochondrial respiratory chain complex I assembly	38	63	2.097e-05
GO:BP	GO:0010257	NADH dehydrogenase complex assembly	38	63	2.097e-05
GO:BP	GO:0005975	carbohydrate metabolic process	224	561	2.161e-05
GO:BP	GO:0022904	respiratory electron transport chain	60	115	2.227e-05
GO:BP	GO:0042326	negative regulation of phosphorylation	116	260	2.231e-05
GO:BP	GO:0001525	angiogenesis	219	547	2.251e-05
GO:BP	GO:0032388	positive regulation of intracellular transport	70	140	2.336e-05
GO:BP	GO:0019646	aerobic electron transport chain	50	91	2.353e-05
GO:BP	GO:0006405	RNA export from nucleus	50	91	2.353e-05
GO:BP	GO:0030038	contractile actin filament bundle assembly	57	108	2.501e-05
GO:BP	GO:0043149	stress fiber assembly	57	108	2.501e-05
GO:BP	GO:0008283	cell population proliferation	709	2015	2.510e-05
GO:BP	GO:0006623	protein targeting to vacuole	31	48	2.532e-05
GO:BP	GO:0051050	positive regulation of transport	322	847	2.538e-05
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	52	96	2.567e-05
GO:BP	GO:1901800	positive regulation of proteasomal protein catabolic process	59	113	2.589e-05
GO:BP	GO:0030099	myeloid cell differentiation	182	443	2.602e-05
GO:BP	GO:0098727	maintenance of cell number	87	184	2.655e-05
GO:BP	GO:0051457	maintenance of protein location in nucleus	19	24	2.677e-05
GO:BP	GO:0043484	regulation of RNA splicing	88	187	2.960e-05
GO:BP	GO:0032507	maintenance of protein location in cell	35	57	2.997e-05
GO:BP	GO:0035051	cardiocyte differentiation	74	151	3.029e-05
GO:BP	GO:0070301	cellular response to hydrogen peroxide	39	66	3.040e-05
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	60	116	3.132e-05
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	28	42	3.168e-05
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	68	136	3.192e-05
GO:BP	GO:0030218	erythrocyte differentiation	68	136	3.192e-05
GO:BP	GO:0042775	mitochondrial ATP synthesis coupled electron transport	53	99	3.202e-05
GO:BP	GO:1903322	positive regulation of protein modification by small protein conjugation or removal	66	131	3.202e-05
GO:BP	GO:0042773	ATP synthesis coupled electron transport	53	99	3.202e-05
GO:BP	GO:0030970	retrograde protein transport, ER to cytosol	21	28	3.371e-05
GO:BP	GO:0036010	protein localization to endosome	21	28	3.371e-05
GO:BP	GO:1903513	endoplasmic reticulum to cytosol transport	21	28	3.371e-05
GO:BP	GO:0099518	vesicle cytoskeletal trafficking	38	64	3.441e-05
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	236	599	3.461e-05
GO:BP	GO:0030336	negative regulation of cell migration	127	292	3.469e-05
GO:BP	GO:0006516	glycoprotein catabolic process	26	38	3.473e-05
GO:BP	GO:0006354	DNA-templated transcription elongation	67	134	3.727e-05
GO:BP	GO:0006644	phospholipid metabolic process	163	392	3.791e-05
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	125	287	3.799e-05
GO:BP	GO:0061564	axon development	211	528	3.859e-05
GO:BP	GO:0009416	response to light stimulus	138	323	4.093e-05
GO:BP	GO:0010595	positive regulation of endothelial cell migration	56	107	4.145e-05
GO:BP	GO:0071453	cellular response to oxygen levels	79	165	4.188e-05
GO:BP	GO:0043086	negative regulation of catalytic activity	127	293	4.232e-05
GO:BP	GO:0032886	regulation of microtubule-based process	117	266	4.430e-05
GO:BP	GO:0042770	signal transduction in response to DNA damage	82	173	4.461e-05
GO:BP	GO:0016239	positive regulation of macroautophagy	48	88	4.740e-05
GO:BP	GO:0006352	DNA-templated transcription initiation	96	210	4.761e-05
GO:BP	GO:0060759	regulation of response to cytokine stimulus	83	176	4.974e-05
GO:BP	GO:0071806	protein transmembrane transport	42	74	5.051e-05
GO:BP	GO:0001933	negative regulation of protein phosphorylation	109	245	5.051e-05
GO:BP	GO:0098732	macromolecule deacylation	35	58	5.052e-05
GO:BP	GO:0010507	negative regulation of autophagy	50	93	5.116e-05
GO:BP	GO:0043542	endothelial cell migration	100	221	5.164e-05
GO:BP	GO:2000146	negative regulation of cell motility	132	308	5.439e-05
GO:BP	GO:0045185	maintenance of protein location	38	65	5.624e-05
GO:BP	GO:0016049	cell growth	195	485	5.709e-05
GO:BP	GO:0072595	maintenance of protein localization in organelle	28	43	6.066e-05
GO:BP	GO:0030900	forebrain development	173	423	6.083e-05
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	60	118	6.083e-05
GO:BP	GO:0007409	axonogenesis	187	463	6.420e-05
GO:BP	GO:0060261	positive regulation of transcription initiation by RNA polymerase II	37	63	6.456e-05
GO:BP	GO:0032006	regulation of TOR signaling	71	146	6.498e-05
GO:BP	GO:0038179	neurotrophin signaling pathway	27	41	6.524e-05
GO:BP	GO:0000266	mitochondrial fission	27	41	6.524e-05
GO:BP	GO:0031397	negative regulation of protein ubiquitination	43	77	6.717e-05
GO:BP	GO:1905475	regulation of protein localization to membrane	89	193	6.830e-05
GO:BP	GO:0010586	miRNA metabolic process	55	106	6.904e-05
GO:BP	GO:0006901	vesicle coating	26	39	6.981e-05
GO:BP	GO:1902117	positive regulation of organelle assembly	48	89	6.981e-05
GO:BP	GO:0040013	negative regulation of locomotion	138	326	7.062e-05
GO:BP	GO:0007517	muscle organ development	152	365	7.114e-05
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	130	304	7.158e-05
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	130	304	7.158e-05
GO:BP	GO:0051091	positive regulation of DNA-binding transcription factor activity	90	196	7.404e-05
GO:BP	GO:0030097	hemopoiesis	362	976	7.685e-05
GO:BP	GO:0045859	regulation of protein kinase activity	165	402	7.737e-05
GO:BP	GO:0042692	muscle cell differentiation	166	405	7.970e-05
GO:BP	GO:0032271	regulation of protein polymerization	91	199	8.056e-05
GO:BP	GO:0048738	cardiac muscle tissue development	104	234	8.546e-05
GO:BP	GO:0006997	nucleus organization	71	147	8.586e-05
GO:BP	GO:0043549	regulation of kinase activity	175	431	8.698e-05
GO:BP	GO:0045862	positive regulation of proteolysis	98	218	8.738e-05
GO:BP	GO:0031122	cytoplasmic microtubule organization	38	66	8.944e-05
GO:BP	GO:0006458	‘de novo’ protein folding	30	48	9.023e-05
GO:BP	GO:0098927	vesicle-mediated transport between endosomal compartments	30	48	9.023e-05
GO:BP	GO:0021987	cerebral cortex development	65	132	9.416e-05
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	57	112	9.809e-05
GO:BP	GO:0043409	negative regulation of MAPK cascade	75	158	1.035e-04
GO:BP	GO:0006360	transcription by RNA polymerase I	40	71	1.050e-04
GO:BP	GO:0046777	protein autophosphorylation	83	179	1.061e-04
GO:BP	GO:0000271	polysaccharide biosynthetic process	33	55	1.091e-04
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	64	130	1.110e-04
GO:BP	GO:0006446	regulation of translational initiation	45	83	1.116e-04
GO:BP	GO:0032984	protein-containing complex disassembly	112	257	1.124e-04
GO:BP	GO:0006611	protein export from nucleus	36	62	1.192e-04
GO:BP	GO:0010594	regulation of endothelial cell migration	79	169	1.203e-04
GO:BP	GO:0031109	microtubule polymerization or depolymerization	67	138	1.230e-04
GO:BP	GO:0000723	telomere maintenance	77	164	1.277e-04
GO:BP	GO:0007032	endosome organization	51	98	1.314e-04
GO:BP	GO:0050770	regulation of axonogenesis	70	146	1.337e-04
GO:BP	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	35	60	1.374e-04
GO:BP	GO:0031032	actomyosin structure organization	95	212	1.383e-04
GO:BP	GO:0051348	negative regulation of transferase activity	78	167	1.410e-04
GO:BP	GO:0060271	cilium assembly	164	403	1.419e-04
GO:BP	GO:0006790	sulfur compound metabolic process	130	308	1.503e-04
GO:BP	GO:0050767	regulation of neurogenesis	155	378	1.520e-04
GO:BP	GO:1905146	lysosomal protein catabolic process	17	22	1.559e-04
GO:BP	GO:0007035	vacuolar acidification	24	36	1.565e-04
GO:BP	GO:0046486	glycerolipid metabolic process	162	398	1.573e-04
GO:BP	GO:0090398	cellular senescence	52	101	1.577e-04
GO:BP	GO:0006399	tRNA metabolic process	94	210	1.606e-04
GO:BP	GO:0051881	regulation of mitochondrial membrane potential	40	72	1.607e-04
GO:BP	GO:1900076	regulation of cellular response to insulin stimulus	40	72	1.607e-04
GO:BP	GO:0051654	establishment of mitochondrion localization	23	34	1.654e-04
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	95	213	1.720e-04
GO:BP	GO:0006622	protein targeting to lysosome	22	32	1.735e-04
GO:BP	GO:1903533	regulation of protein targeting	42	77	1.781e-04
GO:BP	GO:0032527	protein exit from endoplasmic reticulum	29	47	1.781e-04
GO:BP	GO:0034620	cellular response to unfolded protein	49	94	1.804e-04
GO:BP	GO:0051093	negative regulation of developmental process	342	925	1.811e-04
GO:BP	GO:0001667	ameboidal-type cell migration	103	235	1.859e-04
GO:BP	GO:0099173	postsynapse organization	107	246	1.903e-04
GO:BP	GO:0045739	positive regulation of DNA repair	66	137	1.911e-04
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	71	150	1.947e-04
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	79	171	1.976e-04
GO:BP	GO:0044782	cilium organization	173	431	2.036e-04
GO:BP	GO:0010639	negative regulation of organelle organization	145	352	2.142e-04
GO:BP	GO:0045597	positive regulation of cell differentiation	326	879	2.149e-04
GO:BP	GO:0044770	cell cycle phase transition	208	532	2.156e-04
GO:BP	GO:0055007	cardiac muscle cell differentiation	58	117	2.156e-04
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	54	107	2.204e-04
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	27	43	2.218e-04
GO:BP	GO:0043547	positive regulation of GTPase activity	65	135	2.239e-04
GO:BP	GO:0022411	cellular component disassembly	178	446	2.250e-04
GO:BP	GO:0035148	tube formation	70	148	2.275e-04
GO:BP	GO:0003281	ventricular septum development	40	73	2.423e-04
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	40	73	2.423e-04
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	66	138	2.514e-04
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	79	172	2.514e-04
GO:BP	GO:0061462	protein localization to lysosome	34	59	2.514e-04
GO:BP	GO:0104004	cellular response to environmental stimulus	140	339	2.521e-04
GO:BP	GO:0071214	cellular response to abiotic stimulus	140	339	2.521e-04
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	49	95	2.535e-04
GO:BP	GO:0009101	glycoprotein biosynthetic process	126	300	2.572e-04
GO:BP	GO:0031503	protein-containing complex localization	95	215	2.618e-04
GO:BP	GO:0035601	protein deacylation	30	50	2.658e-04
GO:BP	GO:0070085	glycosylation	106	245	2.658e-04
GO:BP	GO:0006486	protein glycosylation	99	226	2.698e-04
GO:BP	GO:0043413	macromolecule glycosylation	99	226	2.698e-04
GO:BP	GO:0007265	Ras protein signal transduction	60	123	2.813e-04
GO:BP	GO:0031113	regulation of microtubule polymerization	36	64	2.921e-04
GO:BP	GO:1904375	regulation of protein localization to cell periphery	70	149	2.946e-04
GO:BP	GO:1901524	regulation of mitophagy	24	37	2.958e-04
GO:BP	GO:0008637	apoptotic mitochondrial changes	52	103	3.009e-04
GO:BP	GO:0032092	positive regulation of protein binding	29	48	3.009e-04
GO:BP	GO:0072583	clathrin-dependent endocytosis	29	48	3.009e-04
GO:BP	GO:0038202	TORC1 signaling	52	103	3.009e-04
GO:BP	GO:0150115	cell-substrate junction organization	52	103	3.009e-04
GO:BP	GO:0010968	regulation of microtubule nucleation	15	19	3.247e-04
GO:BP	GO:0016925	protein sumoylation	38	69	3.275e-04
GO:BP	GO:0001558	regulation of cell growth	163	406	3.373e-04
GO:BP	GO:0043039	tRNA aminoacylation	28	46	3.418e-04
GO:BP	GO:0050684	regulation of mRNA processing	64	134	3.437e-04
GO:BP	GO:0048762	mesenchymal cell differentiation	108	252	3.557e-04
GO:BP	GO:0042982	amyloid precursor protein metabolic process	40	74	3.578e-04
GO:BP	GO:0071456	cellular response to hypoxia	67	142	3.642e-04
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	21	31	3.670e-04
GO:BP	GO:0060562	epithelial tube morphogenesis	138	336	3.852e-04
GO:BP	GO:0043436	oxoacid metabolic process	334	909	3.853e-04
GO:BP	GO:1903146	regulation of autophagy of mitochondrion	27	44	3.855e-04
GO:BP	GO:0044088	regulation of vacuole organization	34	60	3.922e-04
GO:BP	GO:0030200	heparan sulfate proteoglycan catabolic process	9	9	3.930e-04
GO:BP	GO:0160063	multi-pass transmembrane protein insertion into ER membrane	9	9	3.930e-04
GO:BP	GO:0070841	inclusion body assembly	18	25	3.967e-04
GO:BP	GO:0043393	regulation of protein binding	56	114	3.974e-04
GO:BP	GO:0071478	cellular response to radiation	82	182	3.978e-04
GO:BP	GO:0072665	protein localization to vacuole	46	89	4.082e-04
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	52	104	4.125e-04
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	80	177	4.310e-04
GO:BP	GO:0048013	ephrin receptor signaling pathway	30	51	4.354e-04
GO:BP	GO:1990090	cellular response to nerve growth factor stimulus	30	51	4.354e-04
GO:BP	GO:0071482	cellular response to light stimulus	59	122	4.368e-04
GO:BP	GO:0060485	mesenchyme development	132	320	4.393e-04
GO:BP	GO:0062012	regulation of small molecule metabolic process	132	320	4.393e-04
GO:BP	GO:0046854	phosphatidylinositol phosphate biosynthetic process	36	65	4.408e-04
GO:BP	GO:0034605	cellular response to heat	36	65	4.408e-04
GO:BP	GO:0072594	establishment of protein localization to organelle	250	661	4.487e-04
GO:BP	GO:0042327	positive regulation of phosphorylation	197	506	4.487e-04
GO:BP	GO:0006650	glycerophospholipid metabolic process	128	309	4.540e-04
GO:BP	GO:0051960	regulation of nervous system development	180	457	4.567e-04
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	51	102	4.824e-04
GO:BP	GO:0061157	mRNA destabilization	51	102	4.824e-04
GO:BP	GO:0006406	mRNA export from nucleus	38	70	4.837e-04
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	65	138	4.940e-04
GO:BP	GO:0006082	organic acid metabolic process	335	915	5.043e-04
GO:BP	GO:0060284	regulation of cell development	312	847	5.504e-04
GO:BP	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	52	105	5.616e-04
GO:BP	GO:0036294	cellular response to decreased oxygen levels	69	149	5.670e-04
GO:BP	GO:0006984	ER-nucleus signaling pathway	28	47	5.688e-04
GO:BP	GO:0043038	amino acid activation	28	47	5.688e-04
GO:BP	GO:0001959	regulation of cytokine-mediated signaling pathway	75	165	5.823e-04
GO:BP	GO:0016242	negative regulation of macroautophagy	23	36	5.951e-04
GO:BP	GO:0010761	fibroblast migration	31	54	6.051e-04
GO:BP	GO:0000910	cytokinesis	85	192	6.068e-04
GO:BP	GO:0120034	positive regulation of plasma membrane bounded cell projection assembly	55	113	6.244e-04
GO:BP	GO:0021915	neural tube development	73	160	6.267e-04
GO:BP	GO:0003279	cardiac septum development	53	108	6.438e-04
GO:BP	GO:0032231	regulation of actin filament bundle assembly	51	103	6.598e-04
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	43	83	6.612e-04
GO:BP	GO:0072666	establishment of protein localization to vacuole	36	66	6.642e-04
GO:BP	GO:0030167	proteoglycan catabolic process	13	16	6.650e-04
GO:BP	GO:0001934	positive regulation of protein phosphorylation	188	483	6.662e-04
GO:BP	GO:0014812	muscle cell migration	45	88	6.693e-04
GO:BP	GO:0009615	response to virus	164	414	6.916e-04
GO:BP	GO:0000959	mitochondrial RNA metabolic process	30	52	6.948e-04
GO:BP	GO:0045197	establishment or maintenance of epithelial cell apical/basal polarity	30	52	6.948e-04
GO:BP	GO:0031648	protein destabilization	30	52	6.948e-04
GO:BP	GO:0035751	regulation of lysosomal lumen pH	21	32	7.089e-04
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	61	129	7.155e-04
GO:BP	GO:0140352	export from cell	338	928	7.242e-04
GO:BP	GO:0010976	positive regulation of neuron projection development	72	158	7.262e-04
GO:BP	GO:0032101	regulation of response to external stimulus	389	1082	7.262e-04
GO:BP	GO:1903214	regulation of protein targeting to mitochondrion	26	43	7.290e-04
GO:BP	GO:0006418	tRNA aminoacylation for protein translation	26	43	7.290e-04
GO:BP	GO:0009250	glucan biosynthetic process	26	43	7.290e-04
GO:BP	GO:0005978	glycogen biosynthetic process	26	43	7.290e-04
GO:BP	GO:0042127	regulation of cell population proliferation	586	1685	7.335e-04
GO:BP	GO:0050779	RNA destabilization	52	106	7.463e-04
GO:BP	GO:0110020	regulation of actomyosin structure organization	50	101	7.652e-04
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	35	64	7.658e-04
GO:BP	GO:0046903	secretion	359	992	7.658e-04
GO:BP	GO:0007044	cell-substrate junction assembly	48	96	7.744e-04
GO:BP	GO:1903432	regulation of TORC1 signaling	48	96	7.744e-04
GO:BP	GO:1901652	response to peptide	349	962	7.744e-04
GO:BP	GO:0003205	cardiac chamber development	76	169	7.745e-04
GO:BP	GO:0051492	regulation of stress fiber assembly	46	91	7.777e-04
GO:BP	GO:0170036	import into the mitochondrion	29	50	7.908e-04
GO:BP	GO:0035088	establishment or maintenance of apical/basal cell polarity	32	57	7.937e-04
GO:BP	GO:0051058	negative regulation of small GTPase mediated signal transduction	32	57	7.937e-04
GO:BP	GO:0061245	establishment or maintenance of bipolar cell polarity	32	57	7.937e-04
GO:BP	GO:0050435	amyloid-beta metabolic process	32	57	7.937e-04
GO:BP	GO:0047497	mitochondrion transport along microtubule	19	28	7.964e-04
GO:BP	GO:0034643	establishment of mitochondrion localization, microtubule-mediated	19	28	7.964e-04
GO:BP	GO:1901798	positive regulation of signal transduction by p53 class mediator	19	28	7.964e-04
GO:BP	GO:0035330	regulation of hippo signaling	25	41	8.153e-04
GO:BP	GO:0070534	protein K63-linked ubiquitination	37	69	8.156e-04
GO:BP	GO:0071498	cellular response to fluid shear stress	15	20	8.257e-04
GO:BP	GO:0007039	protein catabolic process in the vacuole	18	26	8.336e-04
GO:BP	GO:0045947	negative regulation of translational initiation	16	22	8.555e-04
GO:BP	GO:0007042	lysosomal lumen acidification	17	24	8.555e-04
GO:BP	GO:0075522	IRES-dependent viral translational initiation	10	11	8.578e-04
GO:BP	GO:0051099	positive regulation of binding	51	104	8.626e-04
GO:BP	GO:0007254	JNK cascade	78	175	8.810e-04
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	41	79	8.860e-04
GO:BP	GO:0016601	Rac protein signal transduction	28	48	9.015e-04
GO:BP	GO:0060606	tube closure	45	89	9.044e-04
GO:BP	GO:0032543	mitochondrial translation	61	130	9.046e-04
GO:BP	GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process	31	55	9.149e-04
GO:BP	GO:0032204	regulation of telomere maintenance	54	112	9.446e-04
GO:BP	GO:0006520	amino acid metabolic process	122	297	9.789e-04
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	52	107	9.821e-04
GO:BP	GO:0051092	positive regulation of NF-kappaB transcription factor activity	57	120	1.013e-03
GO:BP	GO:0051222	positive regulation of protein transport	108	258	1.015e-03
GO:BP	GO:0003018	vascular process in circulatory system	113	272	1.021e-03
GO:BP	GO:0031667	response to nutrient levels	196	510	1.024e-03
GO:BP	GO:0040008	regulation of growth	228	604	1.034e-03
GO:BP	GO:0061614	miRNA transcription	40	77	1.037e-03
GO:BP	GO:0090316	positive regulation of intracellular protein transport	48	97	1.037e-03
GO:BP	GO:0018107	peptidyl-threonine phosphorylation	40	77	1.037e-03
GO:BP	GO:0032259	methylation	100	236	1.049e-03
GO:BP	GO:0009791	post-embryonic development	46	92	1.050e-03
GO:BP	GO:0032273	positive regulation of protein polymerization	46	92	1.050e-03
GO:BP	GO:0140238	presynaptic endocytosis	44	87	1.052e-03
GO:BP	GO:0048545	response to steroid hormone	137	340	1.052e-03
GO:BP	GO:1990089	response to nerve growth factor	30	53	1.052e-03
GO:BP	GO:0051403	stress-activated MAPK cascade	30	53	1.052e-03
GO:BP	GO:0043123	positive regulation of canonical NF-kappaB signal transduction	92	214	1.052e-03
GO:BP	GO:0072175	epithelial tube formation	63	136	1.083e-03
GO:BP	GO:0050807	regulation of synapse organization	126	309	1.083e-03
GO:BP	GO:0007051	spindle organization	89	206	1.097e-03
GO:BP	GO:0006665	sphingolipid metabolic process	75	168	1.097e-03
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	66	144	1.100e-03
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	66	144	1.100e-03
GO:BP	GO:0035264	multicellular organism growth	72	160	1.105e-03
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	51	105	1.136e-03
GO:BP	GO:0032922	circadian regulation of gene expression	37	70	1.165e-03
GO:BP	GO:0048863	stem cell differentiation	103	245	1.172e-03
GO:BP	GO:0055082	intracellular chemical homeostasis	270	730	1.183e-03
GO:BP	GO:0045861	negative regulation of proteolysis	67	147	1.194e-03
GO:BP	GO:0036465	synaptic vesicle recycling	47	95	1.203e-03
GO:BP	GO:0008089	anterograde axonal transport	29	51	1.216e-03
GO:BP	GO:0097581	lamellipodium organization	45	90	1.221e-03
GO:BP	GO:2000628	regulation of miRNA metabolic process	45	90	1.221e-03
GO:BP	GO:0048041	focal adhesion assembly	43	85	1.229e-03
GO:BP	GO:0034333	adherens junction assembly	11	13	1.258e-03
GO:BP	GO:1904152	regulation of retrograde protein transport, ER to cytosol	11	13	1.258e-03
GO:BP	GO:0048199	vesicle targeting, to, from or within Golgi	21	33	1.258e-03
GO:BP	GO:0003174	mitral valve development	11	13	1.258e-03
GO:BP	GO:0034097	response to cytokine	342	947	1.270e-03
GO:BP	GO:0031398	positive regulation of protein ubiquitination	52	108	1.274e-03
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	57	121	1.288e-03
GO:BP	GO:0034612	response to tumor necrosis factor	97	229	1.304e-03
GO:BP	GO:0019752	carboxylic acid metabolic process	322	887	1.304e-03
GO:BP	GO:0050803	regulation of synapse structure or activity	128	316	1.312e-03
GO:BP	GO:0072657	protein localization to membrane	302	827	1.319e-03
GO:BP	GO:0034446	substrate adhesion-dependent cell spreading	50	103	1.321e-03
GO:BP	GO:0045022	early endosome to late endosome transport	25	42	1.325e-03
GO:BP	GO:0006476	protein deacetylation	25	42	1.325e-03
GO:BP	GO:0031589	cell-substrate adhesion	142	356	1.327e-03
GO:BP	GO:0038127	ERBB signaling pathway	60	129	1.327e-03
GO:BP	GO:0010628	positive regulation of gene expression	429	1212	1.329e-03
GO:BP	GO:0042987	amyloid precursor protein catabolic process	31	56	1.357e-03
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	48	98	1.357e-03
GO:BP	GO:1901799	negative regulation of proteasomal protein catabolic process	31	56	1.357e-03
GO:BP	GO:0001822	kidney development	130	322	1.365e-03
GO:BP	GO:0007030	Golgi organization	69	153	1.366e-03
GO:BP	GO:0051085	chaperone cofactor-dependent protein refolding	20	31	1.366e-03
GO:BP	GO:0050769	positive regulation of neurogenesis	103	246	1.366e-03
GO:BP	GO:0051205	protein insertion into membrane	28	49	1.378e-03
GO:BP	GO:1903747	regulation of establishment of protein localization to mitochondrion	28	49	1.378e-03
GO:BP	GO:0032387	negative regulation of intracellular transport	28	49	1.378e-03
GO:BP	GO:2000781	positive regulation of double-strand break repair	46	93	1.382e-03
GO:BP	GO:0043112	receptor metabolic process	38	73	1.382e-03
GO:BP	GO:0010564	regulation of cell cycle process	266	720	1.392e-03
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	58	124	1.396e-03
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	212	560	1.398e-03
GO:BP	GO:0001843	neural tube closure	44	88	1.398e-03
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	212	560	1.398e-03
GO:BP	GO:0008154	actin polymerization or depolymerization	83	191	1.399e-03
GO:BP	GO:0048488	synaptic vesicle endocytosis	42	83	1.405e-03
GO:BP	GO:0007018	microtubule-based movement	184	478	1.405e-03
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	70	156	1.453e-03
GO:BP	GO:0060538	skeletal muscle organ development	84	194	1.476e-03
GO:BP	GO:0090140	regulation of mitochondrial fission	19	29	1.478e-03
GO:BP	GO:0003013	circulatory system process	226	602	1.505e-03
GO:BP	GO:0001841	neural tube formation	49	101	1.519e-03
GO:BP	GO:0009408	response to heat	49	101	1.519e-03
GO:BP	GO:0003231	cardiac ventricle development	59	127	1.525e-03
GO:BP	GO:0051444	negative regulation of ubiquitin-protein transferase activity	12	15	1.525e-03
GO:BP	GO:2000779	regulation of double-strand break repair	65	143	1.573e-03
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	27	47	1.580e-03
GO:BP	GO:0048011	neurotrophin TRK receptor signaling pathway	18	27	1.594e-03
GO:BP	GO:0042026	protein refolding	18	27	1.594e-03
GO:BP	GO:0033143	regulation of intracellular steroid hormone receptor signaling pathway	37	71	1.608e-03
GO:BP	GO:0001952	regulation of cell-matrix adhesion	57	122	1.620e-03
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	43	86	1.635e-03
GO:BP	GO:0010660	regulation of muscle cell apoptotic process	39	76	1.636e-03
GO:BP	GO:1902893	regulation of miRNA transcription	39	76	1.636e-03
GO:BP	GO:0043410	positive regulation of MAPK cascade	176	456	1.638e-03
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	23	38	1.681e-03
GO:BP	GO:0061339	establishment or maintenance of monopolar cell polarity	17	25	1.694e-03
GO:BP	GO:0006998	nuclear envelope organization	32	59	1.701e-03
GO:BP	GO:0010810	regulation of cell-substrate adhesion	92	217	1.769e-03
GO:BP	GO:0035357	peroxisome proliferator activated receptor signaling pathway	16	23	1.773e-03
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	48	99	1.773e-03
GO:BP	GO:0035331	negative regulation of hippo signaling	16	23	1.773e-03
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	53	112	1.810e-03
GO:BP	GO:0033059	cellular pigmentation	34	64	1.810e-03
GO:BP	GO:0044772	mitotic cell cycle phase transition	166	428	1.876e-03
GO:BP	GO:0090559	regulation of membrane permeability	36	69	1.885e-03
GO:BP	GO:0051402	neuron apoptotic process	120	296	1.919e-03
GO:BP	GO:0014909	smooth muscle cell migration	38	74	1.923e-03
GO:BP	GO:0031623	receptor internalization	62	136	1.966e-03
GO:BP	GO:0007266	Rho protein signal transduction	65	144	1.967e-03
GO:BP	GO:0031098	stress-activated protein kinase signaling cascade	31	57	1.987e-03
GO:BP	GO:0030865	cortical cytoskeleton organization	31	57	1.987e-03
GO:BP	GO:0097479	synaptic vesicle localization	31	57	1.987e-03
GO:BP	GO:0045216	cell-cell junction organization	91	215	2.025e-03
GO:BP	GO:0048511	rhythmic process	123	305	2.058e-03
GO:BP	GO:0048598	embryonic morphogenesis	231	620	2.077e-03
GO:BP	GO:0048489	synaptic vesicle transport	25	43	2.092e-03
GO:BP	GO:1990000	amyloid fibril formation	25	43	2.092e-03
GO:BP	GO:0032968	positive regulation of transcription elongation by RNA polymerase II	28	50	2.097e-03
GO:BP	GO:0019079	viral genome replication	60	131	2.103e-03
GO:BP	GO:0034063	stress granule assembly	21	34	2.141e-03
GO:BP	GO:0051647	nucleus localization	21	34	2.141e-03
GO:BP	GO:0022604	regulation of cell morphogenesis	102	246	2.145e-03
GO:BP	GO:0032940	secretion by cell	309	854	2.152e-03
GO:BP	GO:1901888	regulation of cell junction assembly	108	263	2.198e-03
GO:BP	GO:0014910	regulation of smooth muscle cell migration	35	67	2.200e-03
GO:BP	GO:0036446	myofibroblast differentiation	9	10	2.202e-03
GO:BP	GO:0030050	vesicle transport along actin filament	9	10	2.202e-03
GO:BP	GO:0010657	muscle cell apoptotic process	41	82	2.238e-03
GO:BP	GO:0034502	protein localization to chromosome	58	126	2.247e-03
GO:BP	GO:0071229	cellular response to acid chemical	48	100	2.332e-03
GO:BP	GO:1903955	positive regulation of protein targeting to mitochondrion	20	32	2.404e-03
GO:BP	GO:0090317	negative regulation of intracellular protein transport	20	32	2.404e-03
GO:BP	GO:0006513	protein monoubiquitination	27	48	2.433e-03
GO:BP	GO:0001881	receptor recycling	27	48	2.433e-03
GO:BP	GO:0001101	response to acid chemical	65	145	2.443e-03
GO:BP	GO:0008631	intrinsic apoptotic signaling pathway in response to oxidative stress	32	60	2.476e-03
GO:BP	GO:1902652	secondary alcohol metabolic process	69	156	2.572e-03
GO:BP	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	40	80	2.645e-03
GO:BP	GO:0061512	protein localization to cilium	38	75	2.664e-03
GO:BP	GO:1903055	positive regulation of extracellular matrix organization	19	30	2.690e-03
GO:BP	GO:0006643	membrane lipid metabolic process	90	214	2.773e-03
GO:BP	GO:0032438	melanosome organization	23	39	2.773e-03
GO:BP	GO:0007224	smoothened signaling pathway	67	151	2.806e-03
GO:BP	GO:0002183	cytoplasmic translational initiation	26	46	2.840e-03
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	58	127	2.868e-03
GO:BP	GO:0046488	phosphatidylinositol metabolic process	71	162	2.908e-03
GO:BP	GO:0032786	positive regulation of DNA-templated transcription, elongation	31	58	2.915e-03
GO:BP	GO:0051962	positive regulation of nervous system development	119	296	2.915e-03
GO:BP	GO:2001032	regulation of double-strand break repair via nonhomologous end joining	18	28	2.980e-03
GO:BP	GO:0070371	ERK1 and ERK2 cascade	120	299	2.980e-03
GO:BP	GO:0050847	progesterone receptor signaling pathway	10	12	3.099e-03
GO:BP	GO:0099515	actin filament-based transport	10	12	3.099e-03
GO:BP	GO:0003183	mitral valve morphogenesis	10	12	3.099e-03
GO:BP	GO:1905165	regulation of lysosomal protein catabolic process	10	12	3.099e-03
GO:BP	GO:0140627	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway	10	12	3.099e-03
GO:BP	GO:0032007	negative regulation of TOR signaling	35	68	3.103e-03
GO:BP	GO:0150116	regulation of cell-substrate junction organization	35	68	3.103e-03
GO:BP	GO:0030330	DNA damage response, signal transduction by p53 class mediator	28	51	3.165e-03
GO:BP	GO:0051259	protein complex oligomerization	110	271	3.165e-03
GO:BP	GO:0051276	chromosome organization	214	574	3.253e-03
GO:BP	GO:0070198	protein localization to chromosome, telomeric region	17	26	3.260e-03
GO:BP	GO:0005980	glycogen catabolic process	17	26	3.260e-03
GO:BP	GO:0001837	epithelial to mesenchymal transition	74	171	3.419e-03
GO:BP	GO:0008285	negative regulation of cell population proliferation	258	706	3.483e-03
GO:BP	GO:0048661	positive regulation of smooth muscle cell proliferation	42	86	3.483e-03
GO:BP	GO:0003007	heart morphogenesis	108	266	3.513e-03
GO:BP	GO:0061162	establishment of monopolar cell polarity	16	24	3.537e-03
GO:BP	GO:0000027	ribosomal large subunit assembly	16	24	3.537e-03
GO:BP	GO:0007346	regulation of mitotic cell cycle	186	492	3.537e-03
GO:BP	GO:0043153	entrainment of circadian clock by photoperiod	16	24	3.537e-03
GO:BP	GO:1902653	secondary alcohol biosynthetic process	32	61	3.557e-03
GO:BP	GO:0006695	cholesterol biosynthetic process	32	61	3.557e-03
GO:BP	GO:0051100	negative regulation of binding	47	99	3.573e-03
GO:BP	GO:0043045	epigenetic programming of gene expression	21	35	3.609e-03
GO:BP	GO:0010948	negative regulation of cell cycle process	116	289	3.632e-03
GO:BP	GO:0072001	renal system development	131	332	3.642e-03
GO:BP	GO:1901203	positive regulation of extracellular matrix assembly	11	14	3.652e-03
GO:BP	GO:2000785	regulation of autophagosome assembly	27	49	3.678e-03
GO:BP	GO:0014020	primary neural tube formation	45	94	3.750e-03
GO:BP	GO:0035089	establishment of apical/basal cell polarity	15	22	3.766e-03
GO:BP	GO:0045596	negative regulation of cell differentiation	246	671	3.772e-03
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	62	139	3.816e-03
GO:BP	GO:0043200	response to amino acid	59	131	3.860e-03
GO:BP	GO:0032200	telomere organization	81	191	3.895e-03
GO:BP	GO:0043543	protein acylation	43	89	3.911e-03
GO:BP	GO:1901663	quinone biosynthetic process	12	16	3.916e-03
GO:BP	GO:0006517	protein deglycosylation	14	20	3.916e-03
GO:BP	GO:0007519	skeletal muscle tissue development	77	180	3.916e-03
GO:BP	GO:0034497	protein localization to phagophore assembly site	12	16	3.916e-03
GO:BP	GO:0006744	ubiquinone biosynthetic process	12	16	3.916e-03
GO:BP	GO:0051788	response to misfolded protein	14	20	3.916e-03
GO:BP	GO:0044849	estrous cycle	12	16	3.916e-03
GO:BP	GO:0045088	regulation of innate immune response	171	449	3.937e-03
GO:BP	GO:0071218	cellular response to misfolded protein	13	18	3.991e-03
GO:BP	GO:0043604	amide biosynthetic process	74	172	4.091e-03
GO:BP	GO:0071356	cellular response to tumor necrosis factor	87	208	4.102e-03
GO:BP	GO:0033002	muscle cell proliferation	87	208	4.102e-03
GO:BP	GO:0050772	positive regulation of axonogenesis	39	79	4.152e-03
GO:BP	GO:1902017	regulation of cilium assembly	37	74	4.238e-03
GO:BP	GO:0050919	negative chemotaxis	26	47	4.266e-03
GO:BP	GO:0016126	sterol biosynthetic process	35	69	4.266e-03
GO:BP	GO:0008203	cholesterol metabolic process	64	145	4.307e-03
GO:BP	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	49	105	4.320e-03
GO:BP	GO:0051347	positive regulation of transferase activity	118	296	4.320e-03
GO:BP	GO:0043523	regulation of neuron apoptotic process	99	242	4.322e-03
GO:BP	GO:0048753	pigment granule organization	23	40	4.334e-03
GO:BP	GO:0006302	double-strand break repair	126	319	4.334e-03
GO:BP	GO:0007416	synapse assembly	105	259	4.334e-03
GO:BP	GO:0060412	ventricular septum morphogenesis	23	40	4.334e-03
GO:BP	GO:0040029	epigenetic regulation of gene expression	119	299	4.383e-03
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	42	87	4.542e-03
GO:BP	GO:0018210	peptidyl-threonine modification	42	87	4.542e-03
GO:BP	GO:0048878	chemical homeostasis	368	1043	4.568e-03
GO:BP	GO:1903846	positive regulation of cellular response to transforming growth factor beta stimulus	19	31	4.592e-03
GO:BP	GO:0030511	positive regulation of transforming growth factor beta receptor signaling pathway	19	31	4.592e-03
GO:BP	GO:0009299	mRNA transcription	28	52	4.592e-03
GO:BP	GO:0009266	response to temperature stimulus	73	170	4.680e-03
GO:BP	GO:0001738	morphogenesis of a polarized epithelium	30	57	4.841e-03
GO:BP	GO:0003151	outflow tract morphogenesis	38	77	4.860e-03
GO:BP	GO:0032233	positive regulation of actin filament bundle assembly	32	62	4.969e-03
GO:BP	GO:0046626	regulation of insulin receptor signaling pathway	34	67	5.002e-03
GO:BP	GO:0039531	regulation of cytoplasmic pattern recognition receptor signaling pathway	54	119	5.209e-03
GO:BP	GO:0090311	regulation of protein deacetylation	18	29	5.214e-03
GO:BP	GO:0051235	maintenance of location	90	218	5.368e-03
GO:BP	GO:0003158	endothelium development	61	138	5.451e-03
GO:BP	GO:1905477	positive regulation of protein localization to membrane	49	106	5.556e-03
GO:BP	GO:0043433	negative regulation of DNA-binding transcription factor activity	58	130	5.562e-03
GO:BP	GO:0055013	cardiac muscle cell development	39	80	5.564e-03
GO:BP	GO:2000736	regulation of stem cell differentiation	39	80	5.564e-03
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	29	55	5.709e-03
GO:BP	GO:0046902	regulation of mitochondrial membrane permeability	29	55	5.709e-03
GO:BP	GO:0030866	cortical actin cytoskeleton organization	24	43	5.802e-03
GO:BP	GO:1902175	regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	24	43	5.802e-03
GO:BP	GO:1903749	positive regulation of establishment of protein localization to mitochondrion	21	36	5.819e-03
GO:BP	GO:0009251	glucan catabolic process	17	27	5.838e-03
GO:BP	GO:0009648	photoperiodism	17	27	5.838e-03
GO:BP	GO:1904153	negative regulation of retrograde protein transport, ER to cytosol	8	9	5.838e-03
GO:BP	GO:0034214	protein hexamerization	8	9	5.838e-03
GO:BP	GO:0030308	negative regulation of cell growth	74	174	5.908e-03
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	74	174	5.908e-03
GO:BP	GO:0002682	regulation of immune system process	541	1581	6.027e-03
GO:BP	GO:0010906	regulation of glucose metabolic process	45	96	6.301e-03
GO:BP	GO:0007097	nuclear migration	16	25	6.523e-03
GO:BP	GO:0045860	positive regulation of protein kinase activity	97	239	6.523e-03
GO:BP	GO:0035020	regulation of Rac protein signal transduction	16	25	6.523e-03
GO:BP	GO:0030859	polarized epithelial cell differentiation	16	25	6.523e-03
GO:BP	GO:1901659	glycosyl compound biosynthetic process	16	25	6.523e-03
GO:BP	GO:0030148	sphingolipid biosynthetic process	51	112	6.538e-03
GO:BP	GO:0009887	animal organ morphogenesis	366	1042	6.600e-03
GO:BP	GO:1902369	negative regulation of RNA catabolic process	43	91	6.666e-03
GO:BP	GO:0016358	dendrite development	98	242	6.679e-03
GO:BP	GO:0008361	regulation of cell size	77	183	6.684e-03
GO:BP	GO:0034405	response to fluid shear stress	20	34	6.684e-03
GO:BP	GO:0002831	regulation of response to biotic stimulus	200	540	6.838e-03
GO:BP	GO:0070373	negative regulation of ERK1 and ERK2 cascade	34	68	6.866e-03
GO:BP	GO:0022029	telencephalon cell migration	32	63	6.922e-03
GO:BP	GO:0051897	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	78	186	6.944e-03
GO:BP	GO:0001838	embryonic epithelial tube formation	55	123	6.980e-03
GO:BP	GO:0009062	fatty acid catabolic process	49	107	7.018e-03
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	62	142	7.050e-03
GO:BP	GO:0051147	regulation of muscle cell differentiation	62	142	7.050e-03
GO:BP	GO:0071345	cellular response to cytokine stimulus	304	854	7.241e-03
GO:BP	GO:0042063	gliogenesis	136	352	7.298e-03
GO:BP	GO:0033674	positive regulation of kinase activity	102	254	7.304e-03
GO:BP	GO:0030641	regulation of cellular pH	44	94	7.337e-03
GO:BP	GO:1905710	positive regulation of membrane permeability	25	46	7.384e-03
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	25	46	7.384e-03
GO:BP	GO:0001825	blastocyst formation	25	46	7.384e-03
GO:BP	GO:0016051	carbohydrate biosynthetic process	80	192	7.436e-03
GO:BP	GO:0010720	positive regulation of cell development	172	458	7.593e-03
GO:BP	GO:0046710	GDP metabolic process	9	11	7.602e-03
GO:BP	GO:0033145	positive regulation of intracellular steroid hormone receptor signaling pathway	9	11	7.602e-03
GO:BP	GO:0006635	fatty acid beta-oxidation	37	76	7.611e-03
GO:BP	GO:1904377	positive regulation of protein localization to cell periphery	37	76	7.611e-03
GO:BP	GO:0099022	vesicle tethering	19	32	7.633e-03
GO:BP	GO:0071514	genomic imprinting	14	21	7.748e-03
GO:BP	GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	22	39	7.748e-03
GO:BP	GO:0048009	insulin-like growth factor receptor signaling pathway	27	51	7.748e-03
GO:BP	GO:0006120	mitochondrial electron transport, NADH to ubiquinone	27	51	7.748e-03
GO:BP	GO:0046426	negative regulation of receptor signaling pathway via JAK-STAT	14	21	7.748e-03
GO:BP	GO:0010591	regulation of lamellipodium assembly	22	39	7.748e-03
GO:BP	GO:0032872	regulation of stress-activated MAPK cascade	22	39	7.748e-03
GO:BP	GO:1901661	quinone metabolic process	14	21	7.748e-03
GO:BP	GO:1905898	positive regulation of response to endoplasmic reticulum stress	22	39	7.748e-03
GO:BP	GO:1905039	carboxylic acid transmembrane transport	64	148	7.754e-03
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	35	71	7.788e-03
GO:BP	GO:0030032	lamellipodium assembly	35	71	7.788e-03
GO:BP	GO:0031345	negative regulation of cell projection organization	77	184	7.830e-03
GO:BP	GO:1904950	negative regulation of establishment of protein localization	57	129	7.830e-03
GO:BP	GO:0042221	response to chemical	1276	3909	7.830e-03
GO:BP	GO:0009306	protein secretion	145	379	7.830e-03
GO:BP	GO:0021885	forebrain cell migration	33	66	7.934e-03
GO:BP	GO:1990928	response to amino acid starvation	29	56	7.934e-03
GO:BP	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	54	121	7.969e-03
GO:BP	GO:0051898	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	31	61	7.990e-03
GO:BP	GO:0046328	regulation of JNK cascade	61	140	8.007e-03
GO:BP	GO:0007098	centrosome cycle	61	140	8.007e-03
GO:BP	GO:0048675	axon extension	51	113	8.036e-03
GO:BP	GO:0006970	response to osmotic stress	40	84	8.055e-03
GO:BP	GO:0099175	regulation of postsynapse organization	65	151	8.081e-03
GO:BP	GO:1903232	melanosome assembly	13	19	8.188e-03
GO:BP	GO:0046931	pore complex assembly	13	19	8.188e-03
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	13	19	8.188e-03
GO:BP	GO:0097284	hepatocyte apoptotic process	13	19	8.188e-03
GO:BP	GO:0051146	striated muscle cell differentiation	118	301	8.288e-03
GO:BP	GO:0036295	cellular response to increased oxygen levels	10	13	8.378e-03
GO:BP	GO:0010421	hydrogen peroxide-mediated programmed cell death	10	13	8.378e-03
GO:BP	GO:0061795	Golgi lumen acidification	10	13	8.378e-03
GO:BP	GO:0071230	cellular response to amino acid stimulus	43	92	8.385e-03
GO:BP	GO:0051051	negative regulation of transport	156	412	8.425e-03
GO:BP	GO:0034205	amyloid-beta formation	24	44	8.429e-03
GO:BP	GO:0010907	positive regulation of glucose metabolic process	24	44	8.429e-03
GO:BP	GO:0090114	COPII-coated vesicle budding	24	44	8.429e-03
GO:BP	GO:0003206	cardiac chamber morphogenesis	55	124	8.429e-03
GO:BP	GO:0046112	nucleobase biosynthetic process	12	17	8.489e-03
GO:BP	GO:0044790	suppression of viral release by host	12	17	8.489e-03
GO:BP	GO:0036508	protein alpha-1,2-demannosylation	12	17	8.489e-03
GO:BP	GO:0036507	protein demannosylation	12	17	8.489e-03
GO:BP	GO:0090136	epithelial cell-cell adhesion	12	17	8.489e-03
GO:BP	GO:0070071	proton-transporting two-sector ATPase complex assembly	12	17	8.489e-03
GO:BP	GO:0090083	regulation of inclusion body assembly	12	17	8.489e-03
GO:BP	GO:1902176	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	18	30	8.493e-03
GO:BP	GO:0000002	mitochondrial genome maintenance	18	30	8.493e-03
GO:BP	GO:0061684	chaperone-mediated autophagy	11	15	8.572e-03
GO:BP	GO:0034616	response to laminar fluid shear stress	11	15	8.572e-03
GO:BP	GO:0006999	nuclear pore organization	11	15	8.572e-03
GO:BP	GO:1905666	regulation of protein localization to endosome	11	15	8.572e-03
GO:BP	GO:0001503	ossification	162	430	8.618e-03
GO:BP	GO:1904760	regulation of myofibroblast differentiation	6	6	8.707e-03
GO:BP	GO:0010935	regulation of macrophage cytokine production	21	37	8.707e-03
GO:BP	GO:0010934	macrophage cytokine production	21	37	8.707e-03
GO:BP	GO:0010616	negative regulation of cardiac muscle adaptation	6	6	8.707e-03
GO:BP	GO:1902904	negative regulation of supramolecular fiber organization	67	157	8.707e-03
GO:BP	GO:1903243	negative regulation of cardiac muscle hypertrophy in response to stress	6	6	8.707e-03
GO:BP	GO:0048205	COPI coating of Golgi vesicle	6	6	8.707e-03
GO:BP	GO:1904816	positive regulation of protein localization to chromosome, telomeric region	6	6	8.707e-03
GO:BP	GO:0046826	negative regulation of protein export from nucleus	6	6	8.707e-03
GO:BP	GO:0048200	Golgi transport vesicle coating	6	6	8.707e-03
GO:BP	GO:0035964	COPI-coated vesicle budding	6	6	8.707e-03
GO:BP	GO:2000765	regulation of cytoplasmic translation	21	37	8.707e-03
GO:BP	GO:0061082	myeloid leukocyte cytokine production	26	49	8.793e-03
GO:BP	GO:0060411	cardiac septum morphogenesis	34	69	8.867e-03
GO:BP	GO:1990138	neuron projection extension	72	171	8.896e-03
GO:BP	GO:0051701	biological process involved in interaction with host	77	185	8.992e-03
GO:BP	GO:0000281	mitotic cytokinesis	44	95	8.992e-03
GO:BP	GO:0016125	sterol metabolic process	68	160	9.027e-03
GO:BP	GO:1903078	positive regulation of protein localization to plasma membrane	32	64	9.045e-03
GO:BP	GO:1901342	regulation of vasculature development	117	299	9.064e-03
GO:BP	GO:0072577	endothelial cell apoptotic process	30	59	9.115e-03
GO:BP	GO:0009451	RNA modification	73	174	9.224e-03
GO:BP	GO:0099177	regulation of trans-synaptic signaling	190	514	9.410e-03
GO:BP	GO:0010212	response to ionizing radiation	61	141	9.483e-03
GO:BP	GO:1903825	organic acid transmembrane transport	65	152	9.492e-03
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	65	152	9.492e-03
GO:BP	GO:0010661	positive regulation of muscle cell apoptotic process	17	28	9.562e-03
GO:BP	GO:0051453	regulation of intracellular pH	42	90	9.574e-03
GO:BP	GO:0009611	response to wounding	208	568	9.576e-03
GO:BP	GO:0033044	regulation of chromosome organization	97	242	9.634e-03
GO:BP	GO:0035794	positive regulation of mitochondrial membrane permeability	23	42	9.638e-03
GO:BP	GO:1990776	response to angiotensin	23	42	9.638e-03
GO:BP	GO:0000077	DNA damage checkpoint signaling	51	114	9.716e-03
GO:BP	GO:0051651	maintenance of location in cell	85	208	9.716e-03
GO:BP	GO:0045926	negative regulation of growth	92	228	9.978e-03
GO:BP	GO:0090162	establishment of epithelial cell polarity	20	35	1.007e-02
GO:BP	GO:0030100	regulation of endocytosis	116	297	1.015e-02
GO:BP	GO:1904018	positive regulation of vasculature development	71	169	1.015e-02
GO:BP	GO:0042789	mRNA transcription by RNA polymerase II	25	47	1.028e-02
GO:BP	GO:0050792	regulation of viral process	67	158	1.033e-02
GO:BP	GO:0051225	spindle assembly	59	136	1.035e-02
GO:BP	GO:0044091	membrane biogenesis	33	67	1.036e-02
GO:BP	GO:0044283	small molecule biosynthetic process	216	593	1.046e-02
GO:BP	GO:0071897	DNA biosynthetic process	72	172	1.051e-02
GO:BP	GO:0062207	regulation of pattern recognition receptor signaling pathway	72	172	1.051e-02
GO:BP	GO:0030838	positive regulation of actin filament polymerization	27	52	1.058e-02
GO:BP	GO:0035592	establishment of protein localization to extracellular region	145	382	1.061e-02
GO:BP	GO:0007160	cell-matrix adhesion	95	237	1.062e-02
GO:BP	GO:0034332	adherens junction organization	29	57	1.065e-02
GO:BP	GO:1902895	positive regulation of miRNA transcription	29	57	1.065e-02
GO:BP	GO:0030041	actin filament polymerization	68	161	1.071e-02
GO:BP	GO:0071692	protein localization to extracellular region	147	388	1.072e-02
GO:BP	GO:1900078	positive regulation of cellular response to insulin stimulus	16	26	1.077e-02
GO:BP	GO:0019081	viral translation	16	26	1.077e-02
GO:BP	GO:0060560	developmental growth involved in morphogenesis	96	240	1.080e-02
GO:BP	GO:0046467	membrane lipid biosynthetic process	64	150	1.081e-02
GO:BP	GO:0001764	neuron migration	78	189	1.082e-02
GO:BP	GO:0006109	regulation of carbohydrate metabolic process	73	175	1.082e-02
GO:BP	GO:0003170	heart valve development	36	75	1.121e-02
GO:BP	GO:1902686	mitochondrial outer membrane permeabilization involved in programmed cell death	22	40	1.121e-02
GO:BP	GO:0048588	developmental cell growth	91	226	1.121e-02
GO:BP	GO:0050804	modulation of chemical synaptic transmission	189	513	1.123e-02
GO:BP	GO:0031570	DNA integrity checkpoint signaling	54	123	1.168e-02
GO:BP	GO:0032088	negative regulation of NF-kappaB transcription factor activity	34	70	1.171e-02
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	34	70	1.171e-02
GO:BP	GO:0062013	positive regulation of small molecule metabolic process	62	145	1.191e-02
GO:BP	GO:0033673	negative regulation of kinase activity	62	145	1.191e-02
GO:BP	GO:0018279	protein N-linked glycosylation via asparagine	24	45	1.198e-02
GO:BP	GO:0035196	miRNA processing	24	45	1.198e-02
GO:BP	GO:2000630	positive regulation of miRNA metabolic process	32	65	1.211e-02
GO:BP	GO:1901673	regulation of mitotic spindle assembly	15	24	1.212e-02
GO:BP	GO:0016311	dephosphorylation	88	218	1.212e-02
GO:BP	GO:0071359	cellular response to dsRNA	15	24	1.212e-02
GO:BP	GO:1904893	negative regulation of receptor signaling pathway via STAT	15	24	1.212e-02
GO:BP	GO:0016079	synaptic vesicle exocytosis	45	99	1.222e-02
GO:BP	GO:0044788	modulation by host of viral process	26	50	1.233e-02
GO:BP	GO:0021795	cerebral cortex cell migration	26	50	1.233e-02
GO:BP	GO:0032506	cytokinetic process	26	50	1.233e-02
GO:BP	GO:0007004	telomere maintenance via telomerase	30	60	1.233e-02
GO:BP	GO:0045444	fat cell differentiation	96	241	1.238e-02
GO:BP	GO:0043489	RNA stabilization	37	78	1.244e-02
GO:BP	GO:0045765	regulation of angiogenesis	114	293	1.258e-02
GO:BP	GO:0002221	pattern recognition receptor signaling pathway	105	267	1.261e-02
GO:BP	GO:0055006	cardiac cell development	40	86	1.294e-02
GO:BP	GO:0010762	regulation of fibroblast migration	21	38	1.306e-02
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	35	73	1.311e-02
GO:BP	GO:0106027	neuron projection organization	43	94	1.315e-02
GO:BP	GO:0065002	intracellular protein transmembrane transport	18	31	1.337e-02
GO:BP	GO:0019082	viral protein processing	18	31	1.337e-02
GO:BP	GO:0034067	protein localization to Golgi apparatus	18	31	1.337e-02
GO:BP	GO:0010977	negative regulation of neuron projection development	57	132	1.366e-02
GO:BP	GO:0097485	neuron projection guidance	95	239	1.402e-02
GO:BP	GO:0051893	regulation of focal adhesion assembly	31	63	1.419e-02
GO:BP	GO:0003229	ventricular cardiac muscle tissue development	31	63	1.419e-02
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	31	63	1.419e-02
GO:BP	GO:0090109	regulation of cell-substrate junction assembly	31	63	1.419e-02
GO:BP	GO:0003012	muscle system process	163	438	1.419e-02
GO:BP	GO:0035383	thioester metabolic process	44	97	1.421e-02
GO:BP	GO:0006637	acyl-CoA metabolic process	44	97	1.421e-02
GO:BP	GO:0071499	cellular response to laminar fluid shear stress	7	8	1.438e-02
GO:BP	GO:0070427	nucleotide-binding oligomerization domain containing 1 signaling pathway	7	8	1.438e-02
GO:BP	GO:2000601	positive regulation of Arp2/3 complex-mediated actin nucleation	7	8	1.438e-02
GO:BP	GO:0048227	plasma membrane to endosome transport	7	8	1.438e-02
GO:BP	GO:0061724	lipophagy	7	8	1.438e-02
GO:BP	GO:0070973	protein localization to endoplasmic reticulum exit site	7	8	1.438e-02
GO:BP	GO:0061383	trabecula morphogenesis	25	48	1.443e-02
GO:BP	GO:0071763	nuclear membrane organization	25	48	1.443e-02
GO:BP	GO:1902459	positive regulation of stem cell population maintenance	25	48	1.443e-02
GO:BP	GO:0019083	viral transcription	27	53	1.456e-02
GO:BP	GO:0034198	cellular response to amino acid starvation	27	53	1.456e-02
GO:BP	GO:0006684	sphingomyelin metabolic process	13	20	1.500e-02
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	48	108	1.500e-02
GO:BP	GO:0090630	activation of GTPase activity	20	36	1.517e-02
GO:BP	GO:0051150	regulation of smooth muscle cell differentiation	20	36	1.517e-02
GO:BP	GO:0046825	regulation of protein export from nucleus	20	36	1.517e-02
GO:BP	GO:0009890	negative regulation of biosynthetic process	926	2813	1.518e-02
GO:BP	GO:0000041	transition metal ion transport	45	100	1.518e-02
GO:BP	GO:0008593	regulation of Notch signaling pathway	45	100	1.518e-02
GO:BP	GO:0000272	polysaccharide catabolic process	17	29	1.533e-02
GO:BP	GO:0034315	regulation of Arp2/3 complex-mediated actin nucleation	17	29	1.533e-02
GO:BP	GO:0001649	osteoblast differentiation	93	234	1.534e-02
GO:BP	GO:0048259	regulation of receptor-mediated endocytosis	52	119	1.542e-02
GO:BP	GO:0045766	positive regulation of angiogenesis	69	166	1.544e-02
GO:BP	GO:0051241	negative regulation of multicellular organismal process	376	1087	1.571e-02
GO:BP	GO:0060760	positive regulation of response to cytokine stimulus	32	66	1.597e-02
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	37	79	1.600e-02
GO:BP	GO:0097494	regulation of vesicle size	12	18	1.633e-02
GO:BP	GO:1904294	positive regulation of ERAD pathway	12	18	1.633e-02
GO:BP	GO:2000641	regulation of early endosome to late endosome transport	12	18	1.633e-02
GO:BP	GO:0006743	ubiquinone metabolic process	12	18	1.633e-02
GO:BP	GO:0032239	regulation of nucleobase-containing compound transport	12	18	1.633e-02
GO:BP	GO:0019896	axonal transport of mitochondrion	12	18	1.633e-02
GO:BP	GO:0000028	ribosomal small subunit assembly	12	18	1.633e-02
GO:BP	GO:0070302	regulation of stress-activated protein kinase signaling cascade	22	41	1.633e-02
GO:BP	GO:0042306	regulation of protein import into nucleus	30	61	1.649e-02
GO:BP	GO:0019318	hexose metabolic process	90	226	1.663e-02
GO:BP	GO:0008064	regulation of actin polymerization or depolymerization	62	147	1.686e-02
GO:BP	GO:0042149	cellular response to glucose starvation	24	46	1.688e-02
GO:BP	GO:0006473	protein acetylation	28	56	1.689e-02
GO:BP	GO:0006487	protein N-linked glycosylation	35	74	1.689e-02
GO:BP	GO:0032008	positive regulation of TOR signaling	35	74	1.689e-02
GO:BP	GO:1902743	regulation of lamellipodium organization	26	51	1.702e-02
GO:BP	GO:0030048	actin filament-based movement	58	136	1.704e-02
GO:BP	GO:0002758	innate immune response-activating signaling pathway	110	284	1.719e-02
GO:BP	GO:0006625	protein targeting to peroxisome	8	10	1.721e-02
GO:BP	GO:1902513	regulation of organelle transport along microtubule	8	10	1.721e-02
GO:BP	GO:0033148	positive regulation of intracellular estrogen receptor signaling pathway	8	10	1.721e-02
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	47	106	1.721e-02
GO:BP	GO:1904667	negative regulation of ubiquitin protein ligase activity	8	10	1.721e-02
GO:BP	GO:0060052	neurofilament cytoskeleton organization	8	10	1.721e-02
GO:BP	GO:1904814	regulation of protein localization to chromosome, telomeric region	8	10	1.721e-02
GO:BP	GO:1901298	regulation of hydrogen peroxide-mediated programmed cell death	8	10	1.721e-02
GO:BP	GO:0048194	Golgi vesicle budding	8	10	1.721e-02
GO:BP	GO:0070862	negative regulation of protein exit from endoplasmic reticulum	8	10	1.721e-02
GO:BP	GO:1900034	regulation of cellular response to heat	11	16	1.736e-02
GO:BP	GO:0043516	regulation of DNA damage response, signal transduction by p53 class mediator	19	34	1.736e-02
GO:BP	GO:0000463	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	11	16	1.736e-02
GO:BP	GO:0043201	response to L-leucine	11	16	1.736e-02
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	16	27	1.736e-02
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	19	34	1.736e-02
GO:BP	GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	11	16	1.736e-02
GO:BP	GO:0030033	microvillus assembly	11	16	1.736e-02
GO:BP	GO:0018198	peptidyl-cysteine modification	19	34	1.736e-02
GO:BP	GO:0002757	immune response-activating signaling pathway	181	494	1.736e-02
GO:BP	GO:0051123	RNA polymerase II preinitiation complex assembly	33	69	1.758e-02
GO:BP	GO:0007411	axon guidance	94	238	1.758e-02
GO:BP	GO:0060429	epithelium development	424	1238	1.781e-02
GO:BP	GO:0031023	microtubule organizing center organization	64	153	1.790e-02
GO:BP	GO:0097468	programmed cell death in response to reactive oxygen species	10	14	1.806e-02
GO:BP	GO:0060816	random inactivation of X chromosome	10	14	1.806e-02
GO:BP	GO:0007008	outer mitochondrial membrane organization	10	14	1.806e-02
GO:BP	GO:1905668	positive regulation of protein localization to endosome	10	14	1.806e-02
GO:BP	GO:1904350	regulation of protein catabolic process in the vacuole	10	14	1.806e-02
GO:BP	GO:0001921	positive regulation of receptor recycling	10	14	1.806e-02
GO:BP	GO:0045040	protein insertion into mitochondrial outer membrane	10	14	1.806e-02
GO:BP	GO:0035358	regulation of peroxisome proliferator activated receptor signaling pathway	10	14	1.806e-02
GO:BP	GO:0006006	glucose metabolic process	75	184	1.808e-02
GO:BP	GO:0034139	regulation of toll-like receptor 3 signaling pathway	9	12	1.810e-02
GO:BP	GO:1905671	regulation of lysosome organization	9	12	1.810e-02
GO:BP	GO:0010172	embryonic body morphogenesis	9	12	1.810e-02
GO:BP	GO:0061723	glycophagy	9	12	1.810e-02
GO:BP	GO:0002011	morphogenesis of an epithelial sheet	31	64	1.828e-02
GO:BP	GO:0005996	monosaccharide metabolic process	98	250	1.860e-02
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	21	39	1.869e-02
GO:BP	GO:0010611	regulation of cardiac muscle hypertrophy	27	54	1.949e-02
GO:BP	GO:1902108	regulation of mitochondrial membrane permeability involved in apoptotic process	23	44	1.949e-02
GO:BP	GO:0044273	sulfur compound catabolic process	23	44	1.949e-02
GO:BP	GO:0008333	endosome to lysosome transport	34	72	1.949e-02
GO:BP	GO:1904263	positive regulation of TORC1 signaling	27	54	1.949e-02
GO:BP	GO:0071824	protein-DNA complex organization	102	262	1.965e-02
GO:BP	GO:0030521	androgen receptor signaling pathway	25	49	1.965e-02
GO:BP	GO:0042073	intraciliary transport	25	49	1.965e-02
GO:BP	GO:0051882	mitochondrial depolarization	15	25	1.976e-02
GO:BP	GO:1904292	regulation of ERAD pathway	15	25	1.976e-02
GO:BP	GO:0097150	neuronal stem cell population maintenance	15	25	1.976e-02
GO:BP	GO:0070861	regulation of protein exit from endoplasmic reticulum	15	25	1.976e-02
GO:BP	GO:0060155	platelet dense granule organization	15	25	1.976e-02
GO:BP	GO:0007059	chromosome segregation	158	427	2.005e-02
GO:BP	GO:0070570	regulation of neuron projection regeneration	18	32	2.009e-02
GO:BP	GO:0070646	protein modification by small protein removal	63	151	2.032e-02
GO:BP	GO:0070050	neuron cellular homeostasis	32	67	2.048e-02
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	97	248	2.085e-02
GO:BP	GO:0008360	regulation of cell shape	59	140	2.085e-02
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	89	225	2.102e-02
GO:BP	GO:0009755	hormone-mediated signaling pathway	89	225	2.102e-02
GO:BP	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	44	99	2.139e-02
GO:BP	GO:0032206	positive regulation of telomere maintenance	35	75	2.139e-02
GO:BP	GO:0032147	activation of protein kinase activity	30	62	2.143e-02
GO:BP	GO:0008347	glial cell migration	30	62	2.143e-02
GO:BP	GO:0044380	protein localization to cytoskeleton	30	62	2.143e-02
GO:BP	GO:0003179	heart valve morphogenesis	30	62	2.143e-02
GO:BP	GO:0001678	intracellular glucose homeostasis	70	171	2.143e-02
GO:BP	GO:0048659	smooth muscle cell proliferation	60	143	2.159e-02
GO:BP	GO:0030155	regulation of cell adhesion	279	794	2.161e-02
GO:BP	GO:0003300	cardiac muscle hypertrophy	38	83	2.165e-02
GO:BP	GO:0006289	nucleotide-excision repair	38	83	2.165e-02
GO:BP	GO:0061448	connective tissue development	112	292	2.176e-02
GO:BP	GO:0071539	protein localization to centrosome	20	37	2.180e-02
GO:BP	GO:0048008	platelet-derived growth factor receptor signaling pathway	28	57	2.216e-02
GO:BP	GO:0014743	regulation of muscle hypertrophy	28	57	2.216e-02
GO:BP	GO:0051452	intracellular pH reduction	28	57	2.216e-02
GO:BP	GO:0001954	positive regulation of cell-matrix adhesion	28	57	2.216e-02
GO:BP	GO:0048010	vascular endothelial growth factor receptor signaling pathway	28	57	2.216e-02
GO:BP	GO:0008015	blood circulation	188	518	2.219e-02
GO:BP	GO:0000963	mitochondrial RNA processing	14	23	2.244e-02
GO:BP	GO:0034249	negative regulation of amide metabolic process	14	23	2.244e-02
GO:BP	GO:0046823	negative regulation of nucleocytoplasmic transport	14	23	2.244e-02
GO:BP	GO:2000114	regulation of establishment of cell polarity	14	23	2.244e-02
GO:BP	GO:0033962	P-body assembly	14	23	2.244e-02
GO:BP	GO:0035773	insulin secretion involved in cellular response to glucose stimulus	33	70	2.252e-02
GO:BP	GO:0019432	triglyceride biosynthetic process	22	42	2.258e-02
GO:BP	GO:0042307	positive regulation of protein import into nucleus	22	42	2.258e-02
GO:BP	GO:0010662	regulation of striated muscle cell apoptotic process	22	42	2.258e-02
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	22	42	2.258e-02
GO:BP	GO:0051496	positive regulation of stress fiber assembly	26	52	2.260e-02
GO:BP	GO:0006812	monoatomic cation transport	368	1069	2.281e-02
GO:BP	GO:0047496	vesicle transport along microtubule	24	47	2.281e-02
GO:BP	GO:0021762	substantia nigra development	24	47	2.281e-02
GO:BP	GO:0061337	cardiac conduction	42	94	2.296e-02
GO:BP	GO:0007155	cell adhesion	516	1530	2.303e-02
GO:BP	GO:1903077	negative regulation of protein localization to plasma membrane	17	30	2.313e-02
GO:BP	GO:0014897	striated muscle hypertrophy	39	86	2.316e-02
GO:BP	GO:0048864	stem cell development	39	86	2.316e-02
GO:BP	GO:0008643	carbohydrate transport	58	138	2.346e-02
GO:BP	GO:2001197	basement membrane assembly involved in embryonic body morphogenesis	5	5	2.346e-02
GO:BP	GO:0038027	apolipoprotein A-I-mediated signaling pathway	5	5	2.346e-02
GO:BP	GO:1904259	regulation of basement membrane assembly involved in embryonic body morphogenesis	5	5	2.346e-02
GO:BP	GO:2000435	negative regulation of protein neddylation	5	5	2.346e-02
GO:BP	GO:0043335	protein unfolding	5	5	2.346e-02
GO:BP	GO:0070370	cellular heat acclimation	5	5	2.346e-02
GO:BP	GO:0010286	heat acclimation	5	5	2.346e-02
GO:BP	GO:1904504	positive regulation of lipophagy	5	5	2.346e-02
GO:BP	GO:1905167	positive regulation of lysosomal protein catabolic process	5	5	2.346e-02
GO:BP	GO:0006469	negative regulation of protein kinase activity	58	138	2.346e-02
GO:BP	GO:1904261	positive regulation of basement membrane assembly involved in embryonic body morphogenesis	5	5	2.346e-02
GO:BP	GO:1904502	regulation of lipophagy	5	5	2.346e-02
GO:BP	GO:0002520	immune system development	81	203	2.346e-02
GO:BP	GO:0046824	positive regulation of nucleocytoplasmic transport	31	65	2.347e-02
GO:BP	GO:0001890	placenta development	63	152	2.347e-02
GO:BP	GO:0006885	regulation of pH	46	105	2.354e-02
GO:BP	GO:0043414	macromolecule methylation	54	127	2.375e-02
GO:BP	GO:1904659	D-glucose transmembrane transport	50	116	2.385e-02
GO:BP	GO:0051961	negative regulation of nervous system development	59	141	2.424e-02
GO:BP	GO:0021766	hippocampus development	43	97	2.424e-02
GO:BP	GO:0002218	activation of innate immune response	116	305	2.480e-02
GO:BP	GO:0099537	trans-synaptic signaling	274	781	2.490e-02
GO:BP	GO:0008645	hexose transmembrane transport	51	119	2.502e-02
GO:BP	GO:0043534	blood vessel endothelial cell migration	51	119	2.502e-02
GO:BP	GO:1902414	protein localization to cell junction	51	119	2.502e-02
GO:BP	GO:0019068	virion assembly	19	35	2.502e-02
GO:BP	GO:0010288	response to lead ion	13	21	2.502e-02
GO:BP	GO:0016556	mRNA modification	13	21	2.502e-02
GO:BP	GO:1904385	cellular response to angiotensin	19	35	2.502e-02
GO:BP	GO:0000462	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	19	35	2.502e-02
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	19	35	2.502e-02
GO:BP	GO:0048147	negative regulation of fibroblast proliferation	19	35	2.502e-02
GO:BP	GO:0044321	response to leptin	13	21	2.502e-02
GO:BP	GO:2001135	regulation of endocytic recycling	13	21	2.502e-02
GO:BP	GO:0060216	definitive hemopoiesis	13	21	2.502e-02
GO:BP	GO:0032102	negative regulation of response to external stimulus	144	388	2.528e-02
GO:BP	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	27	55	2.545e-02
GO:BP	GO:0140374	antiviral innate immune response	27	55	2.545e-02
GO:BP	GO:0002042	cell migration involved in sprouting angiogenesis	27	55	2.545e-02
GO:BP	GO:0002833	positive regulation of response to biotic stimulus	148	400	2.548e-02
GO:BP	GO:0071346	cellular response to type II interferon	44	100	2.556e-02
GO:BP	GO:1904646	cellular response to amyloid-beta	21	40	2.607e-02
GO:BP	GO:0060391	positive regulation of SMAD protein signal transduction	21	40	2.607e-02
GO:BP	GO:0014911	positive regulation of smooth muscle cell migration	21	40	2.607e-02
GO:BP	GO:0090148	membrane fission	23	45	2.639e-02
GO:BP	GO:0010658	striated muscle cell apoptotic process	23	45	2.639e-02
GO:BP	GO:0033688	regulation of osteoblast proliferation	16	28	2.642e-02
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	16	28	2.642e-02
GO:BP	GO:0036296	response to increased oxygen levels	16	28	2.642e-02
GO:BP	GO:0098901	regulation of cardiac muscle cell action potential	16	28	2.642e-02
GO:BP	GO:0030516	regulation of axon extension	38	84	2.647e-02
GO:BP	GO:0043467	regulation of generation of precursor metabolites and energy	57	136	2.647e-02
GO:BP	GO:0030832	regulation of actin filament length	62	150	2.649e-02
GO:BP	GO:0032103	positive regulation of response to external stimulus	228	642	2.741e-02
GO:BP	GO:0045089	positive regulation of innate immune response	139	374	2.745e-02
GO:BP	GO:0048660	regulation of smooth muscle cell proliferation	58	139	2.747e-02
GO:BP	GO:0034220	monoatomic ion transmembrane transport	360	1048	2.796e-02
GO:BP	GO:0006144	purine nucleobase metabolic process	12	19	2.812e-02
GO:BP	GO:0034404	nucleobase-containing small molecule biosynthetic process	12	19	2.812e-02
GO:BP	GO:0090670	RNA localization to Cajal body	12	19	2.812e-02
GO:BP	GO:0090672	telomerase RNA localization	12	19	2.812e-02
GO:BP	GO:0090685	RNA localization to nucleus	12	19	2.812e-02
GO:BP	GO:0009163	nucleoside biosynthetic process	12	19	2.812e-02
GO:BP	GO:1902992	negative regulation of amyloid precursor protein catabolic process	12	19	2.812e-02
GO:BP	GO:0090671	telomerase RNA localization to Cajal body	12	19	2.812e-02
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	28	58	2.866e-02
GO:BP	GO:0008366	axon ensheathment	65	159	2.894e-02
GO:BP	GO:0007272	ensheathment of neurons	65	159	2.894e-02
GO:BP	GO:0021591	ventricular system development	18	33	2.917e-02
GO:BP	GO:0030490	maturation of SSU-rRNA	26	53	2.990e-02
GO:BP	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	31	66	3.027e-02
GO:BP	GO:0021782	glial cell development	56	134	3.037e-02
GO:BP	GO:0034219	carbohydrate transmembrane transport	56	134	3.037e-02
GO:BP	GO:0048145	regulation of fibroblast proliferation	40	90	3.041e-02
GO:BP	GO:0071322	cellular response to carbohydrate stimulus	67	165	3.043e-02
GO:BP	GO:1902110	positive regulation of mitochondrial membrane permeability involved in apoptotic process	20	38	3.043e-02
GO:BP	GO:0070849	response to epidermal growth factor	24	48	3.043e-02
GO:BP	GO:0007549	sex-chromosome dosage compensation	15	26	3.043e-02
GO:BP	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	15	26	3.043e-02
GO:BP	GO:0098916	anterograde trans-synaptic signaling	271	775	3.043e-02
GO:BP	GO:0048208	COPII vesicle coating	15	26	3.043e-02
GO:BP	GO:0006515	protein quality control for misfolded or incompletely synthesized proteins	15	26	3.043e-02
GO:BP	GO:0048207	vesicle targeting, rough ER to cis-Golgi	15	26	3.043e-02
GO:BP	GO:0007268	chemical synaptic transmission	271	775	3.043e-02
GO:BP	GO:0060443	mammary gland morphogenesis	24	48	3.043e-02
GO:BP	GO:0101023	vascular endothelial cell proliferation	15	26	3.043e-02
GO:BP	GO:1905562	regulation of vascular endothelial cell proliferation	15	26	3.043e-02
GO:BP	GO:1905508	protein localization to microtubule organizing center	20	38	3.043e-02
GO:BP	GO:0034453	microtubule anchoring	15	26	3.043e-02
GO:BP	GO:0034331	cell junction maintenance	24	48	3.043e-02
GO:BP	GO:1902229	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	20	38	3.043e-02
GO:BP	GO:0048638	regulation of developmental growth	117	310	3.045e-02
GO:BP	GO:0000075	cell cycle checkpoint signaling	74	185	3.050e-02
GO:BP	GO:0042698	ovulation cycle	34	74	3.050e-02
GO:BP	GO:0070897	transcription preinitiation complex assembly	37	82	3.050e-02
GO:BP	GO:0071364	cellular response to epidermal growth factor stimulus	22	43	3.063e-02
GO:BP	GO:0046839	phospholipid dephosphorylation	22	43	3.063e-02
GO:BP	GO:0061387	regulation of extent of cell growth	44	101	3.083e-02
GO:BP	GO:0060996	dendritic spine development	44	101	3.083e-02
GO:BP	GO:0006895	Golgi to endosome transport	11	17	3.108e-02
GO:BP	GO:0045198	establishment of epithelial cell apical/basal polarity	11	17	3.108e-02
GO:BP	GO:0007063	regulation of sister chromatid cohesion	11	17	3.108e-02
GO:BP	GO:0034349	glial cell apoptotic process	11	17	3.108e-02
GO:BP	GO:0030575	nuclear body organization	11	17	3.108e-02
GO:BP	GO:0071709	membrane assembly	29	61	3.159e-02
GO:BP	GO:0030901	midbrain development	41	93	3.184e-02
GO:BP	GO:0010811	positive regulation of cell-substrate adhesion	53	126	3.184e-02
GO:BP	GO:0014033	neural crest cell differentiation	41	93	3.184e-02
GO:BP	GO:0043473	pigmentation	49	115	3.238e-02
GO:BP	GO:0045446	endothelial cell differentiation	49	115	3.238e-02
GO:BP	GO:0016445	somatic diversification of immunoglobulins	32	69	3.263e-02
GO:BP	GO:0048255	mRNA stabilization	32	69	3.263e-02
GO:BP	GO:0002028	regulation of sodium ion transport	32	69	3.263e-02
GO:BP	GO:0007369	gastrulation	78	197	3.274e-02
GO:BP	GO:0048167	regulation of synaptic plasticity	87	223	3.289e-02
GO:BP	GO:0042060	wound healing	158	433	3.348e-02
GO:BP	GO:0043255	regulation of carbohydrate biosynthetic process	42	96	3.373e-02
GO:BP	GO:0046685	response to arsenic-containing substance	17	31	3.373e-02
GO:BP	GO:0031123	RNA 3’-end processing	42	96	3.373e-02
GO:BP	GO:0045724	positive regulation of cilium assembly	17	31	3.373e-02
GO:BP	GO:0061308	cardiac neural crest cell development involved in heart development	10	15	3.390e-02
GO:BP	GO:0061502	early endosome to recycling endosome transport	6	7	3.390e-02
GO:BP	GO:0050904	diapedesis	6	7	3.390e-02
GO:BP	GO:0046831	regulation of RNA export from nucleus	10	15	3.390e-02
GO:BP	GO:0042780	tRNA 3’-end processing	6	7	3.390e-02
GO:BP	GO:0030091	protein repair	6	7	3.390e-02
GO:BP	GO:0106057	negative regulation of calcineurin-mediated signaling	10	15	3.390e-02
GO:BP	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	10	15	3.390e-02
GO:BP	GO:1905279	regulation of retrograde transport, endosome to Golgi	6	7	3.390e-02
GO:BP	GO:0061307	cardiac neural crest cell differentiation involved in heart development	10	15	3.390e-02
GO:BP	GO:0048298	positive regulation of isotype switching to IgA isotypes	6	7	3.390e-02
GO:BP	GO:0048296	regulation of isotype switching to IgA isotypes	6	7	3.390e-02
GO:BP	GO:0033240	positive regulation of amine metabolic process	6	7	3.390e-02
GO:BP	GO:0010715	regulation of extracellular matrix disassembly	10	15	3.390e-02
GO:BP	GO:0072126	positive regulation of glomerular mesangial cell proliferation	6	7	3.390e-02
GO:BP	GO:0033211	adiponectin-activated signaling pathway	6	7	3.390e-02
GO:BP	GO:0002040	sprouting angiogenesis	55	132	3.390e-02
GO:BP	GO:0006672	ceramide metabolic process	46	107	3.390e-02
GO:BP	GO:0036481	intrinsic apoptotic signaling pathway in response to hydrogen peroxide	6	7	3.390e-02
GO:BP	GO:1901299	negative regulation of hydrogen peroxide-mediated programmed cell death	6	7	3.390e-02
GO:BP	GO:0034334	adherens junction maintenance	6	7	3.390e-02
GO:BP	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	25	51	3.416e-02
GO:BP	GO:0046460	neutral lipid biosynthetic process	25	51	3.416e-02
GO:BP	GO:0046463	acylglycerol biosynthetic process	25	51	3.416e-02
GO:BP	GO:0045824	negative regulation of innate immune response	39	88	3.427e-02
GO:BP	GO:0014896	muscle hypertrophy	39	88	3.427e-02
GO:BP	GO:0007219	Notch signaling pathway	74	186	3.451e-02
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	14	24	3.453e-02
GO:BP	GO:0036119	response to platelet-derived growth factor	14	24	3.453e-02
GO:BP	GO:0051131	chaperone-mediated protein complex assembly	14	24	3.453e-02
GO:BP	GO:0009048	dosage compensation by inactivation of X chromosome	14	24	3.453e-02
GO:BP	GO:0046628	positive regulation of insulin receptor signaling pathway	14	24	3.453e-02
GO:BP	GO:0051560	mitochondrial calcium ion homeostasis	14	24	3.453e-02
GO:BP	GO:0002090	regulation of receptor internalization	33	72	3.477e-02
GO:BP	GO:0032885	regulation of polysaccharide biosynthetic process	19	36	3.477e-02
GO:BP	GO:0002684	positive regulation of immune system process	375	1099	3.477e-02
GO:BP	GO:0006414	translational elongation	36	80	3.477e-02
GO:BP	GO:0006099	tricarboxylic acid cycle	19	36	3.477e-02
GO:BP	GO:1902745	positive regulation of lamellipodium organization	19	36	3.477e-02
GO:BP	GO:0014032	neural crest cell development	36	80	3.477e-02
GO:BP	GO:2000036	regulation of stem cell population maintenance	33	72	3.477e-02
GO:BP	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	23	46	3.486e-02
GO:BP	GO:0035337	fatty-acyl-CoA metabolic process	21	41	3.524e-02
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	21	41	3.524e-02
GO:BP	GO:0071233	cellular response to L-leucine	9	13	3.605e-02
GO:BP	GO:0038203	TORC2 signaling	9	13	3.605e-02
GO:BP	GO:0042761	very long-chain fatty acid biosynthetic process	9	13	3.605e-02
GO:BP	GO:0043558	regulation of translational initiation in response to stress	9	13	3.605e-02
GO:BP	GO:0060612	adipose tissue development	28	59	3.605e-02
GO:BP	GO:0071679	commissural neuron axon guidance	9	13	3.605e-02
GO:BP	GO:0010666	positive regulation of cardiac muscle cell apoptotic process	9	13	3.605e-02
GO:BP	GO:0010766	negative regulation of sodium ion transport	9	13	3.605e-02
GO:BP	GO:0140588	chromatin looping	9	13	3.605e-02
GO:BP	GO:0017062	respiratory chain complex III assembly	9	13	3.605e-02
GO:BP	GO:0098935	dendritic transport	9	13	3.605e-02
GO:BP	GO:0010225	response to UV-C	9	13	3.605e-02
GO:BP	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	9	13	3.605e-02
GO:BP	GO:0055008	cardiac muscle tissue morphogenesis	28	59	3.605e-02
GO:BP	GO:1904380	endoplasmic reticulum mannose trimming	9	13	3.605e-02
GO:BP	GO:0034551	mitochondrial respiratory chain complex III assembly	9	13	3.605e-02
GO:BP	GO:0010663	positive regulation of striated muscle cell apoptotic process	9	13	3.605e-02
GO:BP	GO:0008277	regulation of G protein-coupled receptor signaling pathway	63	155	3.605e-02
GO:BP	GO:0051494	negative regulation of cytoskeleton organization	63	155	3.605e-02
GO:BP	GO:0031347	regulation of defense response	281	809	3.626e-02
GO:BP	GO:0097061	dendritic spine organization	37	83	3.682e-02
GO:BP	GO:0043954	cellular component maintenance	34	75	3.718e-02
GO:BP	GO:0006930	substrate-dependent cell migration, cell extension	7	9	3.718e-02
GO:BP	GO:0014745	negative regulation of muscle adaptation	7	9	3.718e-02
GO:BP	GO:1901724	positive regulation of cell proliferation involved in kidney development	7	9	3.718e-02
GO:BP	GO:1990481	mRNA pseudouridine synthesis	7	9	3.718e-02
GO:BP	GO:1990314	cellular response to insulin-like growth factor stimulus	7	9	3.718e-02
GO:BP	GO:0051561	positive regulation of mitochondrial calcium ion concentration	7	9	3.718e-02
GO:BP	GO:0015886	heme transport	7	9	3.718e-02
GO:BP	GO:0010998	regulation of translational initiation by eIF2 alpha phosphorylation	7	9	3.718e-02
GO:BP	GO:0002191	cap-dependent translational initiation	7	9	3.718e-02
GO:BP	GO:0007220	Notch receptor processing	7	9	3.718e-02
GO:BP	GO:1903332	regulation of protein folding	7	9	3.718e-02
GO:BP	GO:0009113	purine nucleobase biosynthetic process	7	9	3.718e-02
GO:BP	GO:2000678	negative regulation of transcription regulatory region DNA binding	7	9	3.718e-02
GO:BP	GO:2000169	regulation of peptidyl-cysteine S-nitrosylation	7	9	3.718e-02
GO:BP	GO:0035360	positive regulation of peroxisome proliferator activated receptor signaling pathway	7	9	3.718e-02
GO:BP	GO:0032201	telomere maintenance via semi-conservative replication	7	9	3.718e-02
GO:BP	GO:0090085	regulation of protein deubiquitination	8	11	3.726e-02
GO:BP	GO:0046129	purine ribonucleoside biosynthetic process	8	11	3.726e-02
GO:BP	GO:0042451	purine nucleoside biosynthetic process	8	11	3.726e-02
GO:BP	GO:0042455	ribonucleoside biosynthetic process	8	11	3.726e-02
GO:BP	GO:0010807	regulation of synaptic vesicle priming	8	11	3.726e-02
GO:BP	GO:1905383	protein localization to presynapse	8	11	3.726e-02
GO:BP	GO:0061179	negative regulation of insulin secretion involved in cellular response to glucose stimulus	8	11	3.726e-02
GO:BP	GO:0006107	oxaloacetate metabolic process	8	11	3.726e-02
GO:BP	GO:0099532	synaptic vesicle endosomal processing	8	11	3.726e-02
GO:BP	GO:0070372	regulation of ERK1 and ERK2 cascade	104	274	3.726e-02
GO:BP	GO:0006686	sphingomyelin biosynthetic process	8	11	3.726e-02
GO:BP	GO:0023061	signal release	180	501	3.726e-02
GO:BP	GO:0021954	central nervous system neuron development	41	94	3.734e-02
GO:BP	GO:2000351	regulation of endothelial cell apoptotic process	26	54	3.734e-02
GO:BP	GO:0060840	artery development	45	105	3.753e-02
GO:BP	GO:0043392	negative regulation of DNA binding	16	29	3.772e-02
GO:BP	GO:0035265	organ growth	66	164	3.772e-02
GO:BP	GO:0072012	glomerulus vasculature development	16	29	3.772e-02
GO:BP	GO:0043524	negative regulation of neuron apoptotic process	66	164	3.772e-02
GO:BP	GO:0035872	nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway	16	29	3.772e-02
GO:BP	GO:0045116	protein neddylation	16	29	3.772e-02
GO:BP	GO:0048679	regulation of axon regeneration	16	29	3.772e-02
GO:BP	GO:0009649	entrainment of circadian clock	16	29	3.772e-02
GO:BP	GO:0006811	monoatomic ion transport	433	1282	3.791e-02
GO:BP	GO:0099536	synaptic signaling	280	807	3.813e-02
GO:BP	GO:0009743	response to carbohydrate	94	245	3.830e-02
GO:BP	GO:0009746	response to hexose	83	213	3.835e-02
GO:BP	GO:0001824	blastocyst development	50	119	3.835e-02
GO:BP	GO:0022406	membrane docking	38	86	3.839e-02
GO:BP	GO:1900273	positive regulation of long-term synaptic potentiation	13	22	3.861e-02
GO:BP	GO:0036120	cellular response to platelet-derived growth factor stimulus	13	22	3.861e-02
GO:BP	GO:0032482	Rab protein signal transduction	13	22	3.861e-02
GO:BP	GO:0061709	reticulophagy	13	22	3.861e-02
GO:BP	GO:0150105	protein localization to cell-cell junction	13	22	3.861e-02
GO:BP	GO:0016082	synaptic vesicle priming	13	22	3.861e-02
GO:BP	GO:0009605	response to external stimulus	792	2415	3.862e-02
GO:BP	GO:0071526	semaphorin-plexin signaling pathway	24	49	3.863e-02
GO:BP	GO:0045010	actin nucleation	29	62	3.868e-02
GO:BP	GO:0071333	cellular response to glucose stimulus	61	150	3.868e-02
GO:BP	GO:1900024	regulation of substrate adhesion-dependent cell spreading	29	62	3.868e-02
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	32	70	3.929e-02
GO:BP	GO:0048857	neural nucleus development	32	70	3.929e-02
GO:BP	GO:0032376	positive regulation of cholesterol transport	18	34	3.943e-02
GO:BP	GO:0098884	postsynaptic neurotransmitter receptor internalization	18	34	3.943e-02
GO:BP	GO:0140058	neuron projection arborization	18	34	3.943e-02
GO:BP	GO:0140239	postsynaptic endocytosis	18	34	3.943e-02
GO:BP	GO:0032373	positive regulation of sterol transport	18	34	3.943e-02
GO:BP	GO:0090169	regulation of spindle assembly	18	34	3.943e-02
GO:BP	GO:0060603	mammary gland duct morphogenesis	18	34	3.943e-02
GO:BP	GO:0015749	monosaccharide transmembrane transport	51	122	3.943e-02
GO:BP	GO:0009112	nucleobase metabolic process	18	34	3.943e-02
GO:BP	GO:0098662	inorganic cation transmembrane transport	295	854	3.946e-02
GO:BP	GO:0071331	cellular response to hexose stimulus	62	153	3.946e-02
GO:BP	GO:0045646	regulation of erythrocyte differentiation	22	44	3.947e-02
GO:BP	GO:0042398	modified amino acid biosynthetic process	22	44	3.947e-02
GO:BP	GO:0032881	regulation of polysaccharide metabolic process	22	44	3.947e-02
GO:BP	GO:0030258	lipid modification	77	196	3.963e-02
GO:BP	GO:1905476	negative regulation of protein localization to membrane	20	39	3.988e-02
GO:BP	GO:0010665	regulation of cardiac muscle cell apoptotic process	20	39	3.988e-02
GO:BP	GO:0046627	negative regulation of insulin receptor signaling pathway	20	39	3.988e-02
GO:BP	GO:0099068	postsynapse assembly	39	89	4.015e-02
GO:BP	GO:0061515	myeloid cell development	39	89	4.015e-02
GO:BP	GO:0008589	regulation of smoothened signaling pathway	39	89	4.015e-02
GO:BP	GO:0008033	tRNA processing	57	139	4.023e-02
GO:BP	GO:0030323	respiratory tube development	79	202	4.075e-02
GO:BP	GO:0006631	fatty acid metabolic process	146	400	4.111e-02
GO:BP	GO:0051224	negative regulation of protein transport	48	114	4.189e-02
GO:BP	GO:0009749	response to glucose	81	208	4.191e-02
GO:BP	GO:0021761	limbic system development	53	128	4.197e-02
GO:BP	GO:0051145	smooth muscle cell differentiation	30	65	4.197e-02
GO:BP	GO:0043244	regulation of protein-containing complex disassembly	53	128	4.197e-02
GO:BP	GO:0072348	sulfur compound transport	30	65	4.197e-02
GO:BP	GO:0098655	monoatomic cation transmembrane transport	302	877	4.281e-02
GO:BP	GO:0060544	regulation of necroptotic process	15	27	4.362e-02
GO:BP	GO:0060343	trabecula formation	15	27	4.362e-02
GO:BP	GO:0006929	substrate-dependent cell migration	15	27	4.362e-02
GO:BP	GO:0033119	negative regulation of RNA splicing	15	27	4.362e-02
GO:BP	GO:0031468	nuclear membrane reassembly	15	27	4.362e-02
GO:BP	GO:0032878	regulation of establishment or maintenance of cell polarity	15	27	4.362e-02
GO:BP	GO:0034284	response to monosaccharide	85	220	4.388e-02
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	37	84	4.398e-02
GO:BP	GO:2000786	positive regulation of autophagosome assembly	12	20	4.405e-02
GO:BP	GO:1901201	regulation of extracellular matrix assembly	12	20	4.405e-02
GO:BP	GO:0046782	regulation of viral transcription	12	20	4.405e-02
GO:BP	GO:0090141	positive regulation of mitochondrial fission	12	20	4.405e-02
GO:BP	GO:0051851	host-mediated perturbation of symbiont process	45	106	4.426e-02
GO:BP	GO:0050768	negative regulation of neurogenesis	55	134	4.446e-02
GO:BP	GO:0120161	regulation of cold-induced thermogenesis	61	151	4.446e-02
GO:BP	GO:0007052	mitotic spindle organization	55	134	4.446e-02
GO:BP	GO:0035296	regulation of tube diameter	61	151	4.446e-02
GO:BP	GO:0097746	blood vessel diameter maintenance	61	151	4.446e-02
GO:BP	GO:0080164	regulation of nitric oxide metabolic process	28	60	4.482e-02
GO:BP	GO:0010634	positive regulation of epithelial cell migration	23	47	4.485e-02
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	23	47	4.485e-02
GO:BP	GO:0051865	protein autoubiquitination	34	76	4.485e-02
GO:BP	GO:1905515	non-motile cilium assembly	31	68	4.531e-02
GO:BP	GO:1904376	negative regulation of protein localization to cell periphery	17	32	4.612e-02
GO:BP	GO:1902253	regulation of intrinsic apoptotic signaling pathway by p53 class mediator	17	32	4.612e-02
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	894	2745	4.616e-02
GO:BP	GO:0034341	response to type II interferon	51	123	4.627e-02
GO:BP	GO:0010659	cardiac muscle cell apoptotic process	21	42	4.627e-02
GO:BP	GO:0042552	myelination	63	157	4.644e-02
GO:BP	GO:0045324	late endosome to vacuole transport	19	37	4.683e-02
GO:BP	GO:1901655	cellular response to ketone	47	112	4.775e-02
GO:BP	GO:0038066	p38MAPK cascade	26	55	4.775e-02
GO:BP	GO:0072329	monocarboxylic acid catabolic process	52	126	4.775e-02
GO:BP	GO:0033209	tumor necrosis factor-mediated signaling pathway	47	112	4.775e-02
GO:BP	GO:0006836	neurotransmitter transport	82	212	4.775e-02
GO:BP	GO:0043502	regulation of muscle adaptation	35	79	4.780e-02
GO:BP	GO:0002200	somatic diversification of immune receptors	35	79	4.780e-02
GO:BP	GO:1903053	regulation of extracellular matrix organization	29	63	4.886e-02
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	29	63	4.886e-02
GO:BP	GO:0006518	peptide metabolic process	29	63	4.886e-02
KEGG	KEGG:04144	Endocytosis	147	248	1.209e-10
KEGG	KEGG:05012	Parkinson disease	151	265	2.204e-09
KEGG	KEGG:04142	Lysosome	84	131	1.592e-08
KEGG	KEGG:05016	Huntington disease	166	305	1.592e-08
KEGG	KEGG:03010	Ribosome	94	153	2.724e-08
KEGG	KEGG:05010	Alzheimer disease	199	382	2.724e-08
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	237	474	7.445e-08
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	186	363	3.970e-07
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	98	168	3.977e-07
KEGG	KEGG:05132	Salmonella infection	135	249	4.527e-07
KEGG	KEGG:05415	Diabetic cardiomyopathy	110	202	6.832e-06
KEGG	KEGG:04714	Thermogenesis	123	232	8.747e-06
KEGG	KEGG:05171	Coronavirus disease - COVID-19	122	231	1.184e-05
KEGG	KEGG:00190	Oxidative phosphorylation	77	134	2.231e-05
KEGG	KEGG:05208	Chemical carcinogenesis - reactive oxygen species	116	221	2.963e-05
KEGG	KEGG:05168	Herpes simplex virus 1 infection	235	506	8.223e-05
KEGG	KEGG:05020	Prion disease	136	271	8.270e-05
KEGG	KEGG:04140	Autophagy - animal	89	165	1.006e-04
KEGG	KEGG:05212	Pancreatic cancer	47	76	1.523e-04
KEGG	KEGG:04910	Insulin signaling pathway	75	137	2.464e-04
KEGG	KEGG:05210	Colorectal cancer	51	86	3.132e-04
KEGG	KEGG:04932	Non-alcoholic fatty liver disease	82	154	3.617e-04
KEGG	KEGG:05231	Choline metabolism in cancer	56	98	5.136e-04
KEGG	KEGG:04012	ErbB signaling pathway	49	84	7.274e-04
KEGG	KEGG:04148	Efferocytosis	81	156	1.070e-03
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	74	140	1.070e-03
KEGG	KEGG:04722	Neurotrophin signaling pathway	64	118	1.070e-03
KEGG	KEGG:04510	Focal adhesion	101	202	1.070e-03
KEGG	KEGG:04137	Mitophagy - animal	57	103	1.194e-03
KEGG	KEGG:04150	mTOR signaling pathway	80	155	1.366e-03
KEGG	KEGG:05211	Renal cell carcinoma	40	68	2.122e-03
KEGG	KEGG:05017	Spinocerebellar ataxia	73	141	2.213e-03
KEGG	KEGG:04218	Cellular senescence	79	155	2.324e-03
KEGG	KEGG:04360	Axon guidance	90	181	2.608e-03
KEGG	KEGG:05205	Proteoglycans in cancer	100	205	2.912e-03
KEGG	KEGG:05223	Non-small cell lung cancer	41	72	3.992e-03
KEGG	KEGG:05120	Epithelial cell signaling in Helicobacter pylori infection	40	70	4.128e-03
KEGG	KEGG:04392	Hippo signaling pathway - multiple species	20	29	4.181e-03
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	44	79	4.451e-03
KEGG	KEGG:05100	Bacterial invasion of epithelial cells	43	77	4.529e-03
KEGG	KEGG:03013	Nucleocytoplasmic transport	57	108	4.529e-03
KEGG	KEGG:01522	Endocrine resistance	51	95	5.003e-03
KEGG	KEGG:05163	Human cytomegalovirus infection	106	223	5.282e-03
KEGG	KEGG:05110	Vibrio cholerae infection	30	50	5.911e-03
KEGG	KEGG:05220	Chronic myeloid leukemia	42	76	6.379e-03
KEGG	KEGG:05131	Shigellosis	115	246	6.497e-03
KEGG	KEGG:04152	AMPK signaling pathway	61	120	8.903e-03
KEGG	KEGG:04520	Adherens junction	49	93	9.398e-03
KEGG	KEGG:03083	Polycomb repressive complex	45	84	9.398e-03
KEGG	KEGG:05213	Endometrial cancer	33	58	1.050e-02
KEGG	KEGG:04211	Longevity regulating pathway	47	89	1.055e-02
KEGG	KEGG:04146	Peroxisome	44	83	1.306e-02
KEGG	KEGG:00970	Aminoacyl-tRNA biosynthesis	26	44	1.488e-02
KEGG	KEGG:01100	Metabolic pathways	615	1537	1.944e-02
KEGG	KEGG:04666	Fc gamma R-mediated phagocytosis	49	96	1.994e-02
KEGG	KEGG:04010	MAPK signaling pathway	134	301	2.192e-02
KEGG	KEGG:04071	Sphingolipid signaling pathway	59	120	2.354e-02
KEGG	KEGG:05130	Pathogenic Escherichia coli infection	91	197	2.616e-02
KEGG	KEGG:04917	Prolactin signaling pathway	37	70	2.638e-02
KEGG	KEGG:04066	HIF-1 signaling pathway	54	109	2.638e-02
KEGG	KEGG:00604	Glycosphingolipid biosynthesis - ganglio series	11	15	2.638e-02
KEGG	KEGG:04072	Phospholipase D signaling pathway	70	147	2.690e-02
KEGG	KEGG:04933	AGE-RAGE signaling pathway in diabetic complications	50	100	2.703e-02
KEGG	KEGG:04015	Rap1 signaling pathway	96	210	2.703e-02
KEGG	KEGG:03060	Protein export	19	31	2.703e-02
KEGG	KEGG:05214	Glioma	39	75	2.766e-02
KEGG	KEGG:00531	Glycosaminoglycan degradation	13	19	2.766e-02
KEGG	KEGG:04962	Vasopressin-regulated water reabsorption	25	44	2.879e-02
KEGG	KEGG:03015	mRNA surveillance pathway	48	96	2.919e-02
KEGG	KEGG:03250	Viral life cycle - HIV-1	33	62	3.147e-02
KEGG	KEGG:03020	RNA polymerase	20	34	3.716e-02
KEGG	KEGG:04210	Apoptosis	64	135	3.716e-02
KEGG	KEGG:04540	Gap junction	44	88	3.831e-02
KEGG	KEGG:04350	TGF-beta signaling pathway	52	107	3.973e-02
KEGG	KEGG:05165	Human papillomavirus infection	143	330	3.973e-02
KEGG	KEGG:04550	Signaling pathways regulating pluripotency of stem cells	67	143	4.127e-02
KEGG	KEGG:04213	Longevity regulating pathway - multiple species	32	61	4.242e-02
KEGG	KEGG:05235	PD-L1 expression and PD-1 checkpoint pathway in cancer	44	89	4.601e-02
KEGG	KEGG:04931	Insulin resistance	52	108	4.710e-02

# write.csv(table_motif1_GOKEGG_genes, "data/new/table_motif1_GOKEGG_genes.csv")

#GO:BP
table_motif1_genes_GOBP_RUV <- table_motif1_GOKEGG_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif1_genes_GOBP, "data/table_motif1_genes_GOBP.RDS")

table_motif1_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M1 Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG log2cpm Norm Counts Cormotif-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#KEGG
table_motif1_genes_KEGG_RUV <- table_motif1_GOKEGG_genes_RUV %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif1_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M1 DEGs Enriched KEGG Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG log2cpm Norm Counts Cormotif-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#####Motif 2 Genes#####
# motif2_genes_matrix_RUV <- as.matrix(final_genes_2_RUV) 
# colnames(motif2_genes_matrix_RUV) <- c("entrezgene_ID")

# saveRDS(motif2_genes_matrix_RUV, "data/new/RUV/CMF/motif2_genes_matrix_RUV.RDS")

motif2_genes_matrix_RUV <- readRDS("data/new/RUV/CMF/motif2_genes_matrix_RUV.RDS")
length(motif2_genes_matrix_RUV)

[1] 501

#501 genes in this set for motif 2

motif2_mat_GOKEGG_RUV <- gost(query = motif2_genes_matrix_RUV,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif2_GOKEGG_genes_RUV <- gostplot(motif2_mat_GOKEGG_RUV, capped = FALSE, interactive = TRUE)
motif2_GOKEGG_genes_RUV

table_motif2_GOKEGG_genes_RUV <- motif2_mat_GOKEGG_RUV$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif2_GOKEGG_genes_RUV %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0022402	cell cycle process	175	1280	5.510e-90
GO:BP	GO:1903047	mitotic cell cycle process	134	745	6.757e-82
GO:BP	GO:0007049	cell cycle	185	1663	7.203e-81
GO:BP	GO:0000278	mitotic cell cycle	141	892	4.021e-79
GO:BP	GO:0007059	chromosome segregation	97	427	1.026e-67
GO:BP	GO:0000280	nuclear division	95	452	6.218e-63
GO:BP	GO:0051301	cell division	109	658	1.017e-61
GO:BP	GO:0048285	organelle fission	96	500	6.643e-60
GO:BP	GO:0010564	regulation of cell cycle process	111	720	1.112e-59
GO:BP	GO:0098813	nuclear chromosome segregation	80	323	1.652e-58
GO:BP	GO:0140014	mitotic nuclear division	73	282	1.257e-54
GO:BP	GO:0051726	regulation of cell cycle	126	1087	4.813e-54
GO:BP	GO:0051276	chromosome organization	95	574	2.601e-53
GO:BP	GO:0000070	mitotic sister chromatid segregation	62	193	1.623e-52
GO:BP	GO:0000819	sister chromatid segregation	66	234	6.445e-52
GO:BP	GO:0044770	cell cycle phase transition	89	532	3.637e-50
GO:BP	GO:0044772	mitotic cell cycle phase transition	78	428	2.033e-46
GO:BP	GO:1901987	regulation of cell cycle phase transition	75	427	2.437e-43
GO:BP	GO:0006260	DNA replication	63	283	1.360e-42
GO:BP	GO:0007346	regulation of mitotic cell cycle	78	492	7.753e-42
GO:BP	GO:0000075	cell cycle checkpoint signaling	50	185	6.541e-38
GO:BP	GO:0010948	negative regulation of cell cycle process	59	289	1.551e-37
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	62	327	1.551e-37
GO:BP	GO:0051983	regulation of chromosome segregation	43	132	2.536e-36
GO:BP	GO:0006261	DNA-templated DNA replication	46	160	3.571e-36
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	54	248	8.462e-36
GO:BP	GO:1905818	regulation of chromosome separation	35	77	1.831e-35
GO:BP	GO:0045786	negative regulation of cell cycle	63	377	7.789e-35
GO:BP	GO:0006259	DNA metabolic process	98	1005	1.265e-34
GO:BP	GO:0007088	regulation of mitotic nuclear division	40	121	4.455e-34
GO:BP	GO:0051304	chromosome separation	35	84	7.309e-34
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	41	136	3.947e-33
GO:BP	GO:0051310	metaphase chromosome alignment	37	104	7.726e-33
GO:BP	GO:0051783	regulation of nuclear division	42	149	1.230e-32
GO:BP	GO:0090068	positive regulation of cell cycle process	52	262	2.154e-32
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	43	169	2.160e-31
GO:BP	GO:0050000	chromosome localization	38	126	1.096e-30
GO:BP	GO:0051303	establishment of chromosome localization	37	118	1.452e-30
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	42	172	7.227e-30
GO:BP	GO:0007051	spindle organization	45	206	7.918e-30
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	29	62	7.918e-30
GO:BP	GO:0051321	meiotic cell cycle	52	297	1.216e-29
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	46	225	3.511e-29
GO:BP	GO:0051306	mitotic sister chromatid separation	29	65	4.249e-29
GO:BP	GO:0045787	positive regulation of cell cycle	55	351	6.912e-29
GO:BP	GO:0033045	regulation of sister chromatid segregation	34	107	2.629e-28
GO:BP	GO:1903046	meiotic cell cycle process	45	224	3.283e-28
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	26	51	5.082e-28
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	26	51	5.082e-28
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	26	51	5.082e-28
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	26	51	5.082e-28
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	27	57	5.296e-28
GO:BP	GO:0051784	negative regulation of nuclear division	28	65	1.310e-27
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	27	59	1.690e-27
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	26	53	1.714e-27
GO:BP	GO:1905819	negative regulation of chromosome separation	26	53	1.714e-27
GO:BP	GO:0051985	negative regulation of chromosome segregation	26	53	1.714e-27
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	32	97	2.779e-27
GO:BP	GO:0006281	DNA repair	69	621	2.866e-27
GO:BP	GO:0007052	mitotic spindle organization	36	134	3.114e-27
GO:BP	GO:0006974	DNA damage response	83	908	3.686e-27
GO:BP	GO:0071173	spindle assembly checkpoint signaling	25	49	5.060e-27
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	25	49	5.060e-27
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	25	49	5.060e-27
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	32	100	7.532e-27
GO:BP	GO:0031577	spindle checkpoint signaling	25	50	9.617e-27
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	31	93	1.253e-26
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	31	96	3.802e-26
GO:BP	GO:0140013	meiotic nuclear division	41	202	5.875e-26
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	25	54	1.114e-25
GO:BP	GO:0006996	organelle organization	175	3594	2.359e-25
GO:BP	GO:0033044	regulation of chromosome organization	43	242	8.496e-25
GO:BP	GO:0000226	microtubule cytoskeleton organization	68	670	1.344e-24
GO:BP	GO:0044839	cell cycle G2/M phase transition	34	156	1.686e-22
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	32	139	6.208e-22
GO:BP	GO:0007017	microtubule-based process	79	999	9.475e-22
GO:BP	GO:2001251	negative regulation of chromosome organization	27	97	8.380e-21
GO:BP	GO:0006270	DNA replication initiation	19	37	1.540e-20
GO:BP	GO:0051225	spindle assembly	29	136	7.605e-19
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	26	105	1.315e-18
GO:BP	GO:0061982	meiosis I cell cycle process	29	141	2.161e-18
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	21	63	6.248e-18
GO:BP	GO:0051656	establishment of organelle localization	50	491	7.124e-18
GO:BP	GO:0006302	double-strand break repair	40	319	2.430e-17
GO:BP	GO:0045132	meiotic chromosome segregation	24	96	2.855e-17
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	26	118	2.929e-17
GO:BP	GO:1905820	positive regulation of chromosome separation	16	32	5.150e-17
GO:BP	GO:0051640	organelle localization	55	620	5.237e-17
GO:BP	GO:0006310	DNA recombination	41	347	7.288e-17
GO:BP	GO:0000725	recombinational repair	31	193	1.886e-16
GO:BP	GO:0033043	regulation of organelle organization	76	1148	2.120e-16
GO:BP	GO:0033554	cellular response to stress	100	1830	3.261e-16
GO:BP	GO:0051984	positive regulation of chromosome segregation	15	30	5.967e-16
GO:BP	GO:0000724	double-strand break repair via homologous recombination	30	188	7.674e-16
GO:BP	GO:0044786	cell cycle DNA replication	17	45	1.441e-15
GO:BP	GO:0140694	membraneless organelle assembly	43	430	4.952e-15
GO:BP	GO:0033260	nuclear DNA replication	16	41	6.607e-15
GO:BP	GO:0007127	meiosis I	25	133	6.919e-15
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	13	23	1.005e-14
GO:BP	GO:0031570	DNA integrity checkpoint signaling	24	123	1.129e-14
GO:BP	GO:0034508	centromere complex assembly	14	29	1.289e-14
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	23	114	2.159e-14
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	21	93	3.628e-14
GO:BP	GO:0051716	cellular response to stimulus	245	7376	4.997e-14
GO:BP	GO:0007010	cytoskeleton organization	85	1529	5.517e-14
GO:BP	GO:0000727	double-strand break repair via break-induced replication	10	12	6.432e-14
GO:BP	GO:0006275	regulation of DNA replication	23	120	6.738e-14
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	15	40	1.089e-13
GO:BP	GO:0051383	kinetochore organization	12	21	1.118e-13
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	23	124	1.389e-13
GO:BP	GO:0019953	sexual reproduction	69	1122	3.050e-13
GO:BP	GO:0022414	reproductive process	86	1608	3.220e-13
GO:BP	GO:0035556	intracellular signal transduction	128	2965	3.789e-13
GO:BP	GO:0010639	negative regulation of organelle organization	36	352	7.247e-13
GO:BP	GO:0090307	mitotic spindle assembly	18	76	1.561e-12
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	12	25	1.716e-12
GO:BP	GO:1901976	regulation of cell cycle checkpoint	15	48	2.327e-12
GO:BP	GO:0030174	regulation of DNA-templated DNA replication initiation	10	15	2.457e-12
GO:BP	GO:0044771	meiotic cell cycle phase transition	10	15	2.457e-12
GO:BP	GO:0000910	cytokinesis	26	192	4.917e-12
GO:BP	GO:0000281	mitotic cytokinesis	19	95	7.826e-12
GO:BP	GO:1902969	mitotic DNA replication	10	17	1.492e-11
GO:BP	GO:0051052	regulation of DNA metabolic process	41	500	1.706e-11
GO:BP	GO:0050896	response to stimulus	272	8999	5.867e-11
GO:BP	GO:0090231	regulation of spindle checkpoint	11	25	6.242e-11
GO:BP	GO:0032465	regulation of cytokinesis	18	94	7.121e-11
GO:BP	GO:0051231	spindle elongation	9	14	7.127e-11
GO:BP	GO:0007143	female meiotic nuclear division	13	42	1.185e-10
GO:BP	GO:0007098	centrosome cycle	21	140	1.430e-10
GO:BP	GO:0051128	regulation of cellular component organization	105	2433	1.934e-10
GO:BP	GO:0000077	DNA damage checkpoint signaling	19	114	2.213e-10
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	10	21	2.311e-10
GO:BP	GO:0051256	mitotic spindle midzone assembly	8	11	2.702e-10
GO:BP	GO:0030261	chromosome condensation	13	45	3.049e-10
GO:BP	GO:0000022	mitotic spindle elongation	8	12	7.775e-10
GO:BP	GO:0031023	microtubule organizing center organization	21	153	7.775e-10
GO:BP	GO:0051302	regulation of cell division	23	188	9.490e-10
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	19	124	9.706e-10
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	10	24	1.142e-09
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	10	24	1.142e-09
GO:BP	GO:0034502	protein localization to chromosome	19	126	1.267e-09
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	12	41	1.547e-09
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	15	74	1.883e-09
GO:BP	GO:0016043	cellular component organization	248	8184	1.900e-09
GO:BP	GO:0008283	cell population proliferation	89	2015	3.354e-09
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	23	202	3.872e-09
GO:BP	GO:0051255	spindle midzone assembly	8	14	4.198e-09
GO:BP	GO:0050789	regulation of biological process	336	12336	4.430e-09
GO:BP	GO:0065004	protein-DNA complex assembly	25	241	4.452e-09
GO:BP	GO:0071824	protein-DNA complex organization	26	262	5.037e-09
GO:BP	GO:0007062	sister chromatid cohesion	13	57	7.139e-09
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	14	69	7.654e-09
GO:BP	GO:0034080	CENP-A containing chromatin assembly	7	10	7.846e-09
GO:BP	GO:0031055	chromatin remodeling at centromere	7	10	7.846e-09
GO:BP	GO:0006271	DNA strand elongation involved in DNA replication	8	15	8.209e-09
GO:BP	GO:1903083	protein localization to condensed chromosome	8	15	8.209e-09
GO:BP	GO:0034501	protein localization to kinetochore	8	15	8.209e-09
GO:BP	GO:0006468	protein phosphorylation	63	1227	8.209e-09
GO:BP	GO:0044843	cell cycle G1/S phase transition	24	230	8.660e-09
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	14	71	1.088e-08
GO:BP	GO:0032467	positive regulation of cytokinesis	12	50	1.753e-08
GO:BP	GO:0070925	organelle assembly	56	1046	1.915e-08
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	6	7	2.072e-08
GO:BP	GO:0016310	phosphorylation	65	1320	2.183e-08
GO:BP	GO:0051382	kinetochore assembly	8	17	2.857e-08
GO:BP	GO:0071840	cellular component organization or biogenesis	248	8393	2.872e-08
GO:BP	GO:0042770	signal transduction in response to DNA damage	20	173	4.228e-08
GO:BP	GO:0051338	regulation of transferase activity	35	498	4.450e-08
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	7	12	4.542e-08
GO:BP	GO:0050794	regulation of cellular process	324	11946	4.811e-08
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	12	55	5.401e-08
GO:BP	GO:0051653	spindle localization	13	68	6.372e-08
GO:BP	GO:0051445	regulation of meiotic cell cycle	13	68	6.372e-08
GO:BP	GO:0035825	homologous recombination	13	68	6.372e-08
GO:BP	GO:1905821	positive regulation of chromosome condensation	6	8	7.575e-08
GO:BP	GO:0007076	mitotic chromosome condensation	8	19	8.011e-08
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	13	70	9.108e-08
GO:BP	GO:0090232	positive regulation of spindle checkpoint	7	13	9.166e-08
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	12	59	1.216e-07
GO:BP	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	9	28	1.319e-07
GO:BP	GO:0048522	positive regulation of cellular process	186	5920	2.542e-07
GO:BP	GO:0051293	establishment of spindle localization	12	63	2.633e-07
GO:BP	GO:0000212	meiotic spindle organization	8	22	3.076e-07
GO:BP	GO:0065007	biological regulation	337	12743	3.148e-07
GO:BP	GO:0090306	meiotic spindle assembly	7	15	3.183e-07
GO:BP	GO:1902751	positive regulation of cell cycle G2/M phase transition	9	31	3.515e-07
GO:BP	GO:2000241	regulation of reproductive process	20	203	6.005e-07
GO:BP	GO:0051781	positive regulation of cell division	14	98	7.307e-07
GO:BP	GO:0051129	negative regulation of cellular component organization	40	701	9.799e-07
GO:BP	GO:0009314	response to radiation	30	437	1.003e-06
GO:BP	GO:0071897	DNA biosynthetic process	18	172	1.166e-06
GO:BP	GO:0010638	positive regulation of organelle organization	32	492	1.230e-06
GO:BP	GO:0051294	establishment of spindle orientation	10	47	1.391e-06
GO:BP	GO:0051447	negative regulation of meiotic cell cycle	7	18	1.418e-06
GO:BP	GO:2001252	positive regulation of chromosome organization	14	105	1.722e-06
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	9	37	1.831e-06
GO:BP	GO:0090267	positive regulation of mitotic cell cycle spindle assembly checkpoint	6	12	2.039e-06
GO:BP	GO:0007056	spindle assembly involved in female meiosis	6	12	2.039e-06
GO:BP	GO:0060623	regulation of chromosome condensation	6	12	2.039e-06
GO:BP	GO:1901978	positive regulation of cell cycle checkpoint	7	19	2.136e-06
GO:BP	GO:0050790	regulation of catalytic activity	47	928	2.161e-06
GO:BP	GO:0031297	replication fork processing	10	51	3.032e-06
GO:BP	GO:0000076	DNA replication checkpoint signaling	7	20	3.177e-06
GO:BP	GO:0007144	female meiosis I	6	13	3.608e-06
GO:BP	GO:1903490	positive regulation of mitotic cytokinesis	6	13	3.608e-06
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	12	80	3.746e-06
GO:BP	GO:0048518	positive regulation of biological process	189	6264	3.876e-06
GO:BP	GO:0070192	chromosome organization involved in meiotic cell cycle	11	66	4.014e-06
GO:BP	GO:0045143	homologous chromosome segregation	11	67	4.686e-06
GO:BP	GO:0007057	spindle assembly involved in female meiosis I	4	4	4.942e-06
GO:BP	GO:0048856	anatomical structure development	182	5997	5.192e-06
GO:BP	GO:0006950	response to stress	131	3948	5.764e-06
GO:BP	GO:0046385	deoxyribose phosphate biosynthetic process	6	14	5.882e-06
GO:BP	GO:0009263	deoxyribonucleotide biosynthetic process	6	14	5.882e-06
GO:BP	GO:0009265	2’-deoxyribonucleotide biosynthetic process	6	14	5.882e-06
GO:BP	GO:0090235	regulation of metaphase plate congression	6	14	5.882e-06
GO:BP	GO:0040001	establishment of mitotic spindle localization	9	43	6.669e-06
GO:BP	GO:0007275	multicellular organism development	150	4727	8.169e-06
GO:BP	GO:0000731	DNA synthesis involved in DNA repair	9	44	8.169e-06
GO:BP	GO:0051053	negative regulation of DNA metabolic process	15	139	8.891e-06
GO:BP	GO:0032502	developmental process	194	6553	9.316e-06
GO:BP	GO:1902423	regulation of attachment of mitotic spindle microtubules to kinetochore	5	9	1.193e-05
GO:BP	GO:2000242	negative regulation of reproductive process	11	74	1.244e-05
GO:BP	GO:0007131	reciprocal meiotic recombination	10	60	1.346e-05
GO:BP	GO:0140527	reciprocal homologous recombination	10	60	1.346e-05
GO:BP	GO:0045840	positive regulation of mitotic nuclear division	9	47	1.431e-05
GO:BP	GO:1902412	regulation of mitotic cytokinesis	6	16	1.438e-05
GO:BP	GO:0090224	regulation of spindle organization	9	48	1.712e-05
GO:BP	GO:0007154	cell communication	192	6540	2.052e-05
GO:BP	GO:0045859	regulation of protein kinase activity	26	402	2.076e-05
GO:BP	GO:0045842	positive regulation of mitotic metaphase/anaphase transition	6	17	2.143e-05
GO:BP	GO:1902975	mitotic DNA replication initiation	4	5	2.160e-05
GO:BP	GO:0022616	DNA strand elongation	8	37	2.160e-05
GO:BP	GO:1902315	nuclear cell cycle DNA replication initiation	4	5	2.160e-05
GO:BP	GO:1902292	cell cycle DNA replication initiation	4	5	2.160e-05
GO:BP	GO:0110030	regulation of G2/MI transition of meiotic cell cycle	4	5	2.160e-05
GO:BP	GO:0051307	meiotic chromosome separation	5	10	2.185e-05
GO:BP	GO:0045835	negative regulation of meiotic nuclear division	5	10	2.185e-05
GO:BP	GO:0051785	positive regulation of nuclear division	10	64	2.354e-05
GO:BP	GO:0042127	regulation of cell population proliferation	67	1685	2.848e-05
GO:BP	GO:0007292	female gamete generation	16	174	2.944e-05
GO:BP	GO:1902101	positive regulation of metaphase/anaphase transition of cell cycle	6	18	3.011e-05
GO:BP	GO:0048519	negative regulation of biological process	174	5834	3.436e-05
GO:BP	GO:0007165	signal transduction	178	6002	3.444e-05
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	19	242	3.444e-05
GO:BP	GO:0032886	regulation of microtubule-based process	20	266	3.604e-05
GO:BP	GO:0006338	chromatin remodeling	37	725	3.647e-05
GO:BP	GO:0023052	signaling	190	6515	3.697e-05
GO:BP	GO:0051987	positive regulation of attachment of spindle microtubules to kinetochore	5	11	3.760e-05
GO:BP	GO:0065009	regulation of molecular function	61	1496	3.847e-05
GO:BP	GO:0051347	positive regulation of transferase activity	21	296	4.956e-05
GO:BP	GO:0071478	cellular response to radiation	16	182	5.085e-05
GO:BP	GO:0010212	response to ionizing radiation	14	141	5.095e-05
GO:BP	GO:1904666	regulation of ubiquitin protein ligase activity	6	20	5.771e-05
GO:BP	GO:0010032	meiotic chromosome condensation	4	6	5.894e-05
GO:BP	GO:0051649	establishment of localization in cell	75	2010	6.215e-05
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	15	164	6.239e-05
GO:BP	GO:0043549	regulation of kinase activity	26	431	6.661e-05
GO:BP	GO:0007064	mitotic sister chromatid cohesion	7	31	6.851e-05
GO:BP	GO:0060236	regulation of mitotic spindle organization	8	44	7.850e-05
GO:BP	GO:0051298	centrosome duplication	10	74	8.404e-05
GO:BP	GO:0048523	negative regulation of cellular process	167	5629	8.496e-05
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	14	150	1.015e-04
GO:BP	GO:0006796	phosphate-containing compound metabolic process	85	2407	1.062e-04
GO:BP	GO:0006793	phosphorus metabolic process	85	2410	1.110e-04
GO:BP	GO:0008284	positive regulation of cell population proliferation	43	954	1.205e-04
GO:BP	GO:1901994	negative regulation of meiotic cell cycle phase transition	4	7	1.286e-04
GO:BP	GO:0044785	metaphase/anaphase transition of meiotic cell cycle	4	7	1.286e-04
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	15	176	1.417e-04
GO:BP	GO:0001833	inner cell mass cell proliferation	5	14	1.423e-04
GO:BP	GO:0009411	response to UV	14	155	1.441e-04
GO:BP	GO:0040020	regulation of meiotic nuclear division	7	35	1.546e-04
GO:BP	GO:0007276	gamete generation	39	841	1.674e-04
GO:BP	GO:0110032	positive regulation of G2/MI transition of meiotic cell cycle	3	3	1.722e-04
GO:BP	GO:0033316	meiotic spindle assembly checkpoint signaling	3	3	1.722e-04
GO:BP	GO:0071163	DNA replication preinitiation complex assembly	3	3	1.722e-04
GO:BP	GO:0031109	microtubule polymerization or depolymerization	13	138	1.869e-04
GO:BP	GO:0030010	establishment of cell polarity	14	159	1.882e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	34	692	1.891e-04
GO:BP	GO:0032506	cytokinetic process	8	50	1.968e-04
GO:BP	GO:0000132	establishment of mitotic spindle orientation	7	37	2.191e-04
GO:BP	GO:0006325	chromatin organization	40	884	2.191e-04
GO:BP	GO:0009628	response to abiotic stimulus	48	1144	2.191e-04
GO:BP	GO:1902425	positive regulation of attachment of mitotic spindle microtubules to kinetochore	4	8	2.368e-04
GO:BP	GO:1905832	positive regulation of spindle assembly	4	8	2.368e-04
GO:BP	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	4	8	2.368e-04
GO:BP	GO:0048731	system development	126	4053	2.376e-04
GO:BP	GO:0008156	negative regulation of DNA replication	6	26	2.703e-04
GO:BP	GO:0051299	centrosome separation	5	16	2.796e-04
GO:BP	GO:0048513	animal organ development	101	3085	2.835e-04
GO:BP	GO:0071214	cellular response to abiotic stimulus	21	339	3.393e-04
GO:BP	GO:0104004	cellular response to environmental stimulus	21	339	3.393e-04
GO:BP	GO:0048609	multicellular organismal reproductive process	43	1000	3.415e-04
GO:BP	GO:0001932	regulation of protein phosphorylation	36	779	3.698e-04
GO:BP	GO:0051130	positive regulation of cellular component organization	46	1105	3.890e-04
GO:BP	GO:0051054	positive regulation of DNA metabolic process	19	291	3.979e-04
GO:BP	GO:1900264	positive regulation of DNA-directed DNA polymerase activity	4	9	3.979e-04
GO:BP	GO:0000912	assembly of actomyosin apparatus involved in cytokinesis	4	9	3.979e-04
GO:BP	GO:0000915	actomyosin contractile ring assembly	4	9	3.979e-04
GO:BP	GO:1904776	regulation of protein localization to cell cortex	4	9	3.979e-04
GO:BP	GO:0062033	positive regulation of mitotic sister chromatid segregation	4	9	3.979e-04
GO:BP	GO:0071479	cellular response to ionizing radiation	9	72	4.117e-04
GO:BP	GO:0009394	2’-deoxyribonucleotide metabolic process	7	41	4.142e-04
GO:BP	GO:0048144	fibroblast proliferation	11	109	4.207e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	70	1953	4.373e-04
GO:BP	GO:0031399	regulation of protein modification process	44	1049	4.742e-04
GO:BP	GO:0009262	deoxyribonucleotide metabolic process	7	42	4.782e-04
GO:BP	GO:0036297	interstrand cross-link repair	7	42	4.782e-04
GO:BP	GO:0019692	deoxyribose phosphate metabolic process	7	42	4.782e-04
GO:BP	GO:0043009	chordate embryonic development	32	671	5.496e-04
GO:BP	GO:0007099	centriole replication	7	43	5.551e-04
GO:BP	GO:0045740	positive regulation of DNA replication	7	43	5.551e-04
GO:BP	GO:0042325	regulation of phosphorylation	37	830	5.759e-04
GO:BP	GO:1901995	positive regulation of meiotic cell cycle phase transition	3	4	5.937e-04
GO:BP	GO:0044779	meiotic spindle checkpoint signaling	3	4	5.937e-04
GO:BP	GO:0043085	positive regulation of catalytic activity	28	554	6.074e-04
GO:BP	GO:1904668	positive regulation of ubiquitin protein ligase activity	4	10	6.129e-04
GO:BP	GO:0033313	meiotic cell cycle checkpoint signaling	4	10	6.129e-04
GO:BP	GO:2000104	negative regulation of DNA-templated DNA replication	4	10	6.129e-04
GO:BP	GO:0044837	actomyosin contractile ring organization	4	10	6.129e-04
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	8	61	7.623e-04
GO:BP	GO:0033314	mitotic DNA replication checkpoint signaling	4	11	9.377e-04
GO:BP	GO:0072697	protein localization to cell cortex	4	11	9.377e-04
GO:BP	GO:0044093	positive regulation of molecular function	38	884	9.456e-04
GO:BP	GO:0098534	centriole assembly	7	48	1.108e-03
GO:BP	GO:0001832	blastocyst growth	5	22	1.340e-03
GO:BP	GO:1905784	regulation of anaphase-promoting complex-dependent catabolic process	3	5	1.398e-03
GO:BP	GO:1905133	negative regulation of meiotic chromosome separation	3	5	1.398e-03
GO:BP	GO:1902103	negative regulation of metaphase/anaphase transition of meiotic cell cycle	3	5	1.398e-03
GO:BP	GO:0007019	microtubule depolymerization	7	50	1.425e-03
GO:BP	GO:0009966	regulation of signal transduction	96	3034	1.566e-03
GO:BP	GO:0006301	postreplication repair	6	36	1.647e-03
GO:BP	GO:0071695	anatomical structure maturation	17	277	1.988e-03
GO:BP	GO:0009162	deoxyribonucleoside monophosphate metabolic process	5	24	2.036e-03
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	6	38	2.229e-03
GO:BP	GO:0046605	regulation of centrosome cycle	7	54	2.294e-03
GO:BP	GO:0048146	positive regulation of fibroblast proliferation	7	54	2.294e-03
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	5	25	2.470e-03
GO:BP	GO:2000780	negative regulation of double-strand break repair	6	39	2.556e-03
GO:BP	GO:2000105	positive regulation of DNA-templated DNA replication	4	14	2.557e-03
GO:BP	GO:0007100	mitotic centrosome separation	4	14	2.557e-03
GO:BP	GO:0006335	DNA replication-dependent chromatin assembly	3	6	2.585e-03
GO:BP	GO:0009221	pyrimidine deoxyribonucleotide biosynthetic process	3	6	2.585e-03
GO:BP	GO:0046073	dTMP metabolic process	3	6	2.585e-03
GO:BP	GO:1905132	regulation of meiotic chromosome separation	3	6	2.585e-03
GO:BP	GO:0090402	oncogene-induced cell senescence	3	6	2.585e-03
GO:BP	GO:0016321	female meiosis chromosome segregation	3	6	2.585e-03
GO:BP	GO:0042148	DNA strand invasion	3	6	2.585e-03
GO:BP	GO:1902102	regulation of metaphase/anaphase transition of meiotic cell cycle	3	6	2.585e-03
GO:BP	GO:0090166	Golgi disassembly	3	6	2.585e-03
GO:BP	GO:0023051	regulation of signaling	106	3478	2.593e-03
GO:BP	GO:0010646	regulation of cell communication	106	3486	2.823e-03
GO:BP	GO:0007163	establishment or maintenance of cell polarity	15	234	2.846e-03
GO:BP	GO:0019985	translesion synthesis	5	26	2.867e-03
GO:BP	GO:0045738	negative regulation of DNA repair	6	41	3.241e-03
GO:BP	GO:0009130	pyrimidine nucleoside monophosphate biosynthetic process	4	15	3.282e-03
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	7	58	3.410e-03
GO:BP	GO:0072331	signal transduction by p53 class mediator	12	164	3.564e-03
GO:BP	GO:0001824	blastocyst development	10	119	3.764e-03
GO:BP	GO:0036211	protein modification process	89	2846	4.033e-03
GO:BP	GO:2000779	regulation of double-strand break repair	11	143	4.096e-03
GO:BP	GO:0019220	regulation of phosphate metabolic process	38	956	4.096e-03
GO:BP	GO:0072528	pyrimidine-containing compound biosynthetic process	6	43	4.130e-03
GO:BP	GO:0009124	nucleoside monophosphate biosynthetic process	6	43	4.130e-03
GO:BP	GO:0051174	regulation of phosphorus metabolic process	38	957	4.145e-03
GO:BP	GO:0048313	Golgi inheritance	4	16	4.171e-03
GO:BP	GO:0048308	organelle inheritance	4	16	4.171e-03
GO:BP	GO:0051246	regulation of protein metabolic process	63	1855	4.227e-03
GO:BP	GO:0030154	cell differentiation	128	4437	4.784e-03
GO:BP	GO:0048869	cellular developmental process	128	4438	4.817e-03
GO:BP	GO:0044380	protein localization to cytoskeleton	7	62	4.965e-03
GO:BP	GO:0032147	activation of protein kinase activity	7	62	4.965e-03
GO:BP	GO:0006997	nucleus organization	11	147	5.021e-03
GO:BP	GO:0003006	developmental process involved in reproduction	40	1038	5.148e-03
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	6	45	5.161e-03
GO:BP	GO:1905325	regulation of meiosis I spindle assembly checkpoint	2	2	5.599e-03
GO:BP	GO:0110029	negative regulation of meiosis I	2	2	5.599e-03
GO:BP	GO:0099607	lateral attachment of mitotic spindle microtubules to kinetochore	2	2	5.599e-03
GO:BP	GO:1902298	cell cycle DNA replication maintenance of fidelity	2	2	5.599e-03
GO:BP	GO:1990426	mitotic recombination-dependent replication fork processing	2	2	5.599e-03
GO:BP	GO:0014846	esophagus smooth muscle contraction	2	2	5.599e-03
GO:BP	GO:1990505	mitotic DNA replication maintenance of fidelity	2	2	5.599e-03
GO:BP	GO:0031619	homologous chromosome orientation in meiotic metaphase I	2	2	5.599e-03
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	8	83	5.599e-03
GO:BP	GO:0140274	repair of kinetochore microtubule attachment defect	2	2	5.599e-03
GO:BP	GO:0071881	adenylate cyclase-inhibiting adrenergic receptor signaling pathway	2	2	5.599e-03
GO:BP	GO:1905318	meiosis I spindle assembly checkpoint signaling	2	2	5.599e-03
GO:BP	GO:0140273	repair of mitotic kinetochore microtubule attachment defect	2	2	5.599e-03
GO:BP	GO:0045814	negative regulation of gene expression, epigenetic	13	200	5.845e-03
GO:BP	GO:0006939	smooth muscle contraction	9	105	5.954e-03
GO:BP	GO:0031507	heterochromatin formation	11	151	6.014e-03
GO:BP	GO:0010458	exit from mitosis	5	31	6.107e-03
GO:BP	GO:0080090	regulation of primary metabolic process	150	5390	6.107e-03
GO:BP	GO:0007077	mitotic nuclear membrane disassembly	3	8	6.221e-03
GO:BP	GO:0007096	regulation of exit from mitosis	4	18	6.292e-03
GO:BP	GO:0051641	cellular localization	108	3661	6.743e-03
GO:BP	GO:0048608	reproductive structure development	17	314	7.129e-03
GO:BP	GO:0009790	embryo development	42	1135	7.895e-03
GO:BP	GO:0051642	centrosome localization	5	33	8.048e-03
GO:BP	GO:0006221	pyrimidine nucleotide biosynthetic process	5	33	8.048e-03
GO:BP	GO:0061842	microtubule organizing center localization	5	33	8.048e-03
GO:BP	GO:0061458	reproductive system development	17	318	8.087e-03
GO:BP	GO:0031100	animal organ regeneration	7	68	8.087e-03
GO:BP	GO:0046601	positive regulation of centriole replication	3	9	8.931e-03
GO:BP	GO:0046602	regulation of mitotic centrosome separation	3	9	8.931e-03
GO:BP	GO:2000243	positive regulation of reproductive process	8	90	9.099e-03
GO:BP	GO:0034644	cellular response to UV	8	90	9.099e-03
GO:BP	GO:0090169	regulation of spindle assembly	5	34	9.108e-03
GO:BP	GO:0021700	developmental maturation	18	352	9.400e-03
GO:BP	GO:0001701	in utero embryonic development	20	413	9.716e-03
GO:BP	GO:1902410	mitotic cytokinetic process	5	35	1.034e-02
GO:BP	GO:0010332	response to gamma radiation	6	52	1.034e-02
GO:BP	GO:0007018	microtubule-based movement	22	478	1.060e-02
GO:BP	GO:0051443	positive regulation of ubiquitin-protein transferase activity	4	21	1.113e-02
GO:BP	GO:0045137	development of primary sexual characteristics	14	243	1.113e-02
GO:BP	GO:0001556	oocyte maturation	5	36	1.168e-02
GO:BP	GO:0110025	DNA strand resection involved in replication fork processing	3	10	1.219e-02
GO:BP	GO:0007399	nervous system development	80	2604	1.237e-02
GO:BP	GO:0007129	homologous chromosome pairing at meiosis	6	54	1.241e-02
GO:BP	GO:0009129	pyrimidine nucleoside monophosphate metabolic process	4	22	1.316e-02
GO:BP	GO:2000001	regulation of DNA damage checkpoint	4	22	1.316e-02
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	7	75	1.384e-02
GO:BP	GO:0000018	regulation of DNA recombination	10	144	1.420e-02
GO:BP	GO:0071392	cellular response to estradiol stimulus	5	38	1.468e-02
GO:BP	GO:0071312	cellular response to alkaloid	5	38	1.468e-02
GO:BP	GO:0032501	multicellular organismal process	192	7322	1.475e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	56	1.475e-02
GO:BP	GO:0034421	post-translational protein acetylation	2	3	1.493e-02
GO:BP	GO:0006231	dTMP biosynthetic process	2	3	1.493e-02
GO:BP	GO:0009177	pyrimidine deoxyribonucleoside monophosphate biosynthetic process	2	3	1.493e-02
GO:BP	GO:0046599	regulation of centriole replication	4	23	1.526e-02
GO:BP	GO:0009219	pyrimidine deoxyribonucleotide metabolic process	4	23	1.526e-02
GO:BP	GO:0006282	regulation of DNA repair	13	225	1.553e-02
GO:BP	GO:0072711	cellular response to hydroxyurea	3	11	1.566e-02
GO:BP	GO:0009987	cellular process	456	20247	1.566e-02
GO:BP	GO:0009650	UV protection	3	11	1.566e-02
GO:BP	GO:0009176	pyrimidine deoxyribonucleoside monophosphate metabolic process	3	11	1.566e-02
GO:BP	GO:1990918	double-strand break repair involved in meiotic recombination	3	11	1.566e-02
GO:BP	GO:0070601	centromeric sister chromatid cohesion	3	11	1.566e-02
GO:BP	GO:0006029	proteoglycan metabolic process	8	100	1.671e-02
GO:BP	GO:0090398	cellular senescence	8	101	1.777e-02
GO:BP	GO:0009123	nucleoside monophosphate metabolic process	7	79	1.790e-02
GO:BP	GO:0006998	nuclear envelope organization	6	59	1.867e-02
GO:BP	GO:0031401	positive regulation of protein modification process	26	637	1.998e-02
GO:BP	GO:0042276	error-prone translesion synthesis	3	12	2.001e-02
GO:BP	GO:0051081	nuclear membrane disassembly	3	12	2.001e-02
GO:BP	GO:0072710	response to hydroxyurea	3	12	2.001e-02
GO:BP	GO:0008584	male gonad development	10	152	2.001e-02
GO:BP	GO:0014831	gastro-intestinal system smooth muscle contraction	3	12	2.001e-02
GO:BP	GO:0071168	protein localization to chromatin	6	60	2.001e-02
GO:BP	GO:0071493	cellular response to UV-B	3	12	2.001e-02
GO:BP	GO:0046546	development of primary male sexual characteristics	10	153	2.087e-02
GO:BP	GO:0009416	response to light stimulus	16	323	2.226e-02
GO:BP	GO:0043412	macromolecule modification	89	3030	2.267e-02
GO:BP	GO:0007548	sex differentiation	15	294	2.270e-02
GO:BP	GO:0006760	folic acid-containing compound metabolic process	4	26	2.313e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	4	26	2.313e-02
GO:BP	GO:0030866	cortical actin cytoskeleton organization	5	43	2.388e-02
GO:BP	GO:0008406	gonad development	13	238	2.403e-02
GO:BP	GO:0001934	positive regulation of protein phosphorylation	21	483	2.444e-02
GO:BP	GO:0045860	positive regulation of protein kinase activity	13	239	2.481e-02
GO:BP	GO:1903251	multi-ciliated epithelial cell differentiation	3	13	2.486e-02
GO:BP	GO:0048469	cell maturation	12	211	2.486e-02
GO:BP	GO:0030397	membrane disassembly	3	13	2.486e-02
GO:BP	GO:0051493	regulation of cytoskeleton organization	22	517	2.508e-02
GO:BP	GO:0040029	epigenetic regulation of gene expression	15	299	2.602e-02
GO:BP	GO:0051296	establishment of meiotic spindle orientation	2	4	2.648e-02
GO:BP	GO:1901563	response to camptothecin	2	4	2.648e-02
GO:BP	GO:0072757	cellular response to camptothecin	2	4	2.648e-02
GO:BP	GO:0043060	meiotic metaphase I homologous chromosome alignment	2	4	2.648e-02
GO:BP	GO:1905448	positive regulation of mitochondrial ATP synthesis coupled electron transport	2	4	2.648e-02
GO:BP	GO:0009212	pyrimidine deoxyribonucleoside triphosphate biosynthetic process	2	4	2.648e-02
GO:BP	GO:0048583	regulation of response to stimulus	112	3993	2.648e-02
GO:BP	GO:0051754	meiotic sister chromatid cohesion, centromeric	2	4	2.648e-02
GO:BP	GO:0006235	dTTP biosynthetic process	2	4	2.648e-02
GO:BP	GO:0007079	mitotic chromosome movement towards spindle pole	2	4	2.648e-02
GO:BP	GO:0046075	dTTP metabolic process	2	4	2.648e-02
GO:BP	GO:1990086	lens fiber cell apoptotic process	2	4	2.648e-02
GO:BP	GO:0051145	smooth muscle cell differentiation	6	65	2.835e-02
GO:BP	GO:0051446	positive regulation of meiotic cell cycle	4	28	2.913e-02
GO:BP	GO:0033262	regulation of nuclear cell cycle DNA replication	3	14	2.996e-02
GO:BP	GO:0051177	meiotic sister chromatid cohesion	3	14	2.996e-02
GO:BP	GO:0009888	tissue development	63	2032	3.049e-02
GO:BP	GO:0006284	base-excision repair	5	46	3.049e-02
GO:BP	GO:0016477	cell migration	50	1534	3.119e-02
GO:BP	GO:1902117	positive regulation of organelle assembly	7	89	3.198e-02
GO:BP	GO:0035418	protein localization to synapse	7	89	3.198e-02
GO:BP	GO:0000723	telomere maintenance	10	164	3.198e-02
GO:BP	GO:0070977	bone maturation	4	29	3.253e-02
GO:BP	GO:0010165	response to X-ray	4	29	3.253e-02
GO:BP	GO:0006915	apoptotic process	60	1923	3.277e-02
GO:BP	GO:0010824	regulation of centrosome duplication	5	47	3.298e-02
GO:BP	GO:0071773	cellular response to BMP stimulus	10	165	3.298e-02
GO:BP	GO:0071772	response to BMP	10	165	3.298e-02
GO:BP	GO:0048145	regulation of fibroblast proliferation	7	90	3.356e-02
GO:BP	GO:0042752	regulation of circadian rhythm	8	114	3.365e-02
GO:BP	GO:0071763	nuclear membrane organization	5	48	3.558e-02
GO:BP	GO:0044027	negative regulation of gene expression via chromosomal CpG island methylation	3	15	3.558e-02
GO:BP	GO:0043101	purine-containing compound salvage	3	15	3.558e-02
GO:BP	GO:0035860	glial cell-derived neurotrophic factor receptor signaling pathway	3	15	3.558e-02
GO:BP	GO:0001938	positive regulation of endothelial cell proliferation	7	92	3.738e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	7	92	3.738e-02
GO:BP	GO:0033674	positive regulation of kinase activity	13	254	3.817e-02
GO:BP	GO:0042327	positive regulation of phosphorylation	21	506	3.817e-02
GO:BP	GO:0097421	liver regeneration	4	31	4.040e-02
GO:BP	GO:0006297	nucleotide-excision repair, DNA gap filling	2	5	4.052e-02
GO:BP	GO:0071962	mitotic sister chromatid cohesion, centromeric	2	5	4.052e-02
GO:BP	GO:0031536	positive regulation of exit from mitosis	2	5	4.052e-02
GO:BP	GO:0043137	DNA replication, removal of RNA primer	2	5	4.052e-02
GO:BP	GO:0098535	de novo centriole assembly involved in multi-ciliated epithelial cell differentiation	2	5	4.052e-02
GO:BP	GO:0140499	negative regulation of mitotic spindle assembly checkpoint signaling	2	5	4.052e-02
GO:BP	GO:0090233	negative regulation of spindle checkpoint	2	5	4.052e-02
GO:BP	GO:0051311	meiotic metaphase chromosome alignment	2	5	4.052e-02
GO:BP	GO:0061351	neural precursor cell proliferation	10	171	4.078e-02
GO:BP	GO:0050918	positive chemotaxis	6	71	4.097e-02
GO:BP	GO:0012501	programmed cell death	61	1987	4.118e-02
GO:BP	GO:0090399	replicative senescence	3	16	4.152e-02
GO:BP	GO:0051782	negative regulation of cell division	3	16	4.152e-02
GO:BP	GO:0141124	intracellular signaling cassette	59	1912	4.241e-02
GO:BP	GO:0008219	cell death	61	1991	4.268e-02
GO:BP	GO:0042558	pteridine-containing compound metabolic process	4	32	4.399e-02
GO:BP	GO:0042311	vasodilation	5	51	4.406e-02
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	5	51	4.406e-02
GO:BP	GO:0045910	negative regulation of DNA recombination	5	51	4.406e-02
GO:BP	GO:0090102	cochlea development	5	51	4.406e-02
GO:BP	GO:0048468	cell development	83	2876	4.483e-02
GO:BP	GO:0051261	protein depolymerization	8	121	4.529e-02
GO:BP	GO:0002062	chondrocyte differentiation	8	121	4.529e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	93	3288	4.594e-02
GO:BP	GO:0071482	cellular response to light stimulus	8	122	4.738e-02
GO:BP	GO:0002063	chondrocyte development	4	33	4.749e-02
GO:BP	GO:0080135	regulation of cellular response to stress	21	519	4.749e-02
GO:BP	GO:0046661	male sex differentiation	10	176	4.749e-02
GO:BP	GO:0046653	tetrahydrofolate metabolic process	3	17	4.749e-02
GO:BP	GO:0014841	skeletal muscle satellite cell proliferation	3	17	4.749e-02
GO:BP	GO:0031573	mitotic intra-S DNA damage checkpoint signaling	3	17	4.749e-02
GO:BP	GO:0048799	animal organ maturation	4	33	4.749e-02
GO:BP	GO:0043094	metabolic compound salvage	4	33	4.749e-02
GO:BP	GO:0043173	nucleotide salvage	3	17	4.749e-02
GO:BP	GO:0007063	regulation of sister chromatid cohesion	3	17	4.749e-02
GO:BP	GO:0085020	protein K6-linked ubiquitination	3	17	4.749e-02
GO:BP	GO:0007265	Ras protein signal transduction	8	123	4.863e-02
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	7	98	4.872e-02
GO:BP	GO:0046785	microtubule polymerization	7	98	4.872e-02
KEGG	KEGG:04110	Cell cycle	46	157	4.527e-33
KEGG	KEGG:03030	DNA replication	16	36	3.615e-14
KEGG	KEGG:03460	Fanconi anemia pathway	12	54	1.440e-06
KEGG	KEGG:04114	Oocyte meiosis	17	131	4.452e-06
KEGG	KEGG:04914	Progesterone-mediated oocyte maturation	15	102	4.452e-06
KEGG	KEGG:03440	Homologous recombination	10	41	4.452e-06
KEGG	KEGG:04115	p53 signaling pathway	12	74	2.423e-05
KEGG	KEGG:04218	Cellular senescence	16	155	1.585e-04
KEGG	KEGG:04814	Motor proteins	17	193	5.981e-04
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	17	218	2.517e-03
KEGG	KEGG:03410	Base excision repair	7	44	3.885e-03
KEGG	KEGG:03430	Mismatch repair	5	23	6.852e-03
KEGG	KEGG:05222	Small cell lung cancer	9	92	1.611e-02
KEGG	KEGG:00240	Pyrimidine metabolism	7	57	1.611e-02
KEGG	KEGG:01232	Nucleotide metabolism	8	84	3.409e-02
KEGG	KEGG:04512	ECM-receptor interaction	8	89	4.604e-02

# write.csv(table_motif2_GOKEGG_genes, "data/new/table_motif2_GOKEGG_genes.csv")

#GO:BP
table_motif2_genes_GOBP_RUV <- table_motif2_GOKEGG_genes_RUV %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif2_genes_GOBP, "data/table_motif2_genes_GOBP.RDS")

table_motif2_genes_GOBP_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M2 Enriched GO:BP Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG log2cpm Norm Counts Cormotif-5.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#KEGG
table_motif2_genes_KEGG_RUV <- table_motif2_GOKEGG_genes_RUV %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif2_genes_KEGG_RUV %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M2 DEGs Enriched KEGG Terms RUVs")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG log2cpm Norm Counts Cormotif-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#now take these final gene sets for each motif - clustlike + p.post consensus genes

#clust1_genes_RUV
#clust2_genes_RUV


# library(gprofiler2)
#####Motif 1 Gene Set#####
# motif1_genes_matrix_RUV_clust <- as.matrix(clust1_genes_RUV)
# colnames(motif1_genes_matrix_RUV_clust) <- c("entrezgene_ID")

# saveRDS(motif1_genes_matrix_RUV_clust, "data/new/RUV/CMF/motif1_genes_matrix_RUV_clustlike.RDS")

motif1_genes_matrix_RUV_clust <- readRDS("data/new/RUV/CMF/motif1_genes_matrix_RUV_clustlike.RDS")
length(motif1_genes_matrix_RUV_clust)

[1] 13600

#13600 genes in this set for motif 1

motif1_mat_GOKEGG_RUV_clust <- gost(query = motif1_genes_matrix_RUV_clust,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif1_GOKEGG_genes_RUV_clust <- gostplot(motif1_mat_GOKEGG_RUV_clust, capped = FALSE, interactive = TRUE)
motif1_GOKEGG_genes_RUV_clust

table_motif1_GOKEGG_genes_RUV_clust <- motif1_mat_GOKEGG_RUV_clust$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif1_GOKEGG_genes_RUV_clust %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0019538	protein metabolic process	3572	4721	6.575e-248
GO:BP	GO:0080090	regulation of primary metabolic process	3961	5390	1.663e-235
GO:BP	GO:0006996	organelle organization	2772	3594	5.707e-204
GO:BP	GO:0043412	macromolecule modification	2363	3030	1.811e-180
GO:BP	GO:0048522	positive regulation of cellular process	4134	5920	2.252e-172
GO:BP	GO:0048518	positive regulation of biological process	4329	6264	4.298e-169
GO:BP	GO:0046907	intracellular transport	1214	1381	4.334e-164
GO:BP	GO:0036211	protein modification process	2200	2846	7.300e-158
GO:BP	GO:0051641	cellular localization	2713	3661	1.013e-154
GO:BP	GO:0009056	catabolic process	2054	2639	4.245e-152
GO:BP	GO:0019219	regulation of nucleobase-containing compound metabolic process	2911	3990	1.232e-151
GO:BP	GO:0065007	biological regulation	7872	12743	8.913e-149
GO:BP	GO:0051179	localization	3836	5555	2.391e-142
GO:BP	GO:0050789	regulation of biological process	7630	12336	2.999e-140
GO:BP	GO:0051252	regulation of RNA metabolic process	2693	3687	4.054e-139
GO:BP	GO:0051649	establishment of localization in cell	1611	2010	2.010e-137
GO:BP	GO:0050794	regulation of cellular process	7402	11946	4.870e-134
GO:BP	GO:0006810	transport	3110	4407	4.569e-129
GO:BP	GO:0033554	cellular response to stress	1474	1830	3.304e-128
GO:BP	GO:0006351	DNA-templated transcription	2579	3549	1.662e-127
GO:BP	GO:0009057	macromolecule catabolic process	1187	1417	1.738e-125
GO:BP	GO:0051128	regulation of cellular component organization	1864	2433	4.395e-124
GO:BP	GO:0070727	cellular macromolecule localization	2086	2782	4.661e-123
GO:BP	GO:0033036	macromolecule localization	2367	3228	9.817e-123
GO:BP	GO:0008104	protein localization	2075	2770	1.402e-121
GO:BP	GO:0006355	regulation of DNA-templated transcription	2470	3409	1.103e-118
GO:BP	GO:2001141	regulation of RNA biosynthetic process	2481	3428	2.229e-118
GO:BP	GO:0009893	positive regulation of metabolic process	2578	3597	2.059e-115
GO:BP	GO:0019222	regulation of metabolic process	4610	7035	2.064e-113
GO:BP	GO:0007275	multicellular organism development	3255	4727	3.294e-112
GO:BP	GO:0023051	regulation of signaling	2494	3478	2.199e-111
GO:BP	GO:0010646	regulation of cell communication	2498	3486	4.892e-111
GO:BP	GO:0015031	protein transport	1180	1444	2.458e-109
GO:BP	GO:0035556	intracellular signal transduction	2165	2965	1.692e-107
GO:BP	GO:0051246	regulation of protein metabolic process	1450	1855	3.472e-106
GO:BP	GO:0009966	regulation of signal transduction	2201	3034	1.188e-104
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	2355	3288	3.280e-103
GO:BP	GO:0032502	developmental process	4297	6553	4.417e-103
GO:BP	GO:0071705	nitrogen compound transport	1488	1923	7.698e-103
GO:BP	GO:0006796	phosphate-containing compound metabolic process	1799	2407	5.284e-102
GO:BP	GO:0006793	phosphorus metabolic process	1800	2410	1.296e-101
GO:BP	GO:0048856	anatomical structure development	3968	5997	4.295e-101
GO:BP	GO:0051234	establishment of localization	3337	4928	4.577e-100
GO:BP	GO:0048583	regulation of response to stimulus	2770	3993	1.190e-97
GO:BP	GO:0030163	protein catabolic process	874	1030	2.765e-97
GO:BP	GO:0048731	system development	2799	4053	2.940e-95
GO:BP	GO:0006366	transcription by RNA polymerase II	1964	2711	6.088e-91
GO:BP	GO:0060255	regulation of macromolecule metabolic process	4215	6492	4.354e-90
GO:BP	GO:0009894	regulation of catabolic process	866	1040	2.886e-87
GO:BP	GO:0045935	positive regulation of nucleobase-containing compound metabolic process	1525	2036	4.086e-86
GO:BP	GO:0051603	proteolysis involved in protein catabolic process	683	786	5.449e-85
GO:BP	GO:0006357	regulation of transcription by RNA polymerase II	1863	2578	4.008e-84
GO:BP	GO:0016192	vesicle-mediated transport	1224	1592	5.152e-80
GO:BP	GO:0007399	nervous system development	1864	2604	1.815e-78
GO:BP	GO:0043687	post-translational protein modification	839	1027	3.781e-76
GO:BP	GO:0006886	intracellular protein transport	596	686	9.810e-74
GO:BP	GO:0051254	positive regulation of RNA metabolic process	1367	1835	1.107e-73
GO:BP	GO:0070647	protein modification by small protein conjugation or removal	798	975	5.319e-73
GO:BP	GO:0030030	cell projection organization	1234	1631	5.602e-73
GO:BP	GO:0032446	protein modification by small protein conjugation	713	853	1.056e-72
GO:BP	GO:0045184	establishment of protein localization	1427	1937	1.249e-71
GO:BP	GO:0043632	modification-dependent macromolecule catabolic process	562	643	1.423e-71
GO:BP	GO:0048523	negative regulation of cellular process	3645	5629	2.042e-71
GO:BP	GO:0120036	plasma membrane bounded cell projection organization	1201	1588	1.010e-70
GO:BP	GO:0019941	modification-dependent protein catabolic process	557	638	1.581e-70
GO:BP	GO:0048519	negative regulation of biological process	3757	5834	7.605e-70
GO:BP	GO:1902531	regulation of intracellular signal transduction	1432	1953	1.287e-69
GO:BP	GO:0061919	process utilizing autophagic mechanism	525	597	7.456e-69
GO:BP	GO:0006914	autophagy	525	597	7.456e-69
GO:BP	GO:0010498	proteasomal protein catabolic process	485	543	1.244e-68
GO:BP	GO:0033043	regulation of organelle organization	907	1148	1.665e-68
GO:BP	GO:0006511	ubiquitin-dependent protein catabolic process	547	628	1.897e-68
GO:BP	GO:0006412	translation	614	727	8.566e-66
GO:BP	GO:0042254	ribosome biogenesis	312	323	2.994e-65
GO:BP	GO:0009891	positive regulation of biosynthetic process	1877	2696	1.271e-63
GO:BP	GO:0070925	organelle assembly	829	1046	1.789e-63
GO:BP	GO:1902680	positive regulation of RNA biosynthetic process	1255	1699	1.789e-63
GO:BP	GO:0045893	positive regulation of DNA-templated transcription	1253	1697	3.430e-63
GO:BP	GO:0044087	regulation of cellular component biogenesis	801	1011	4.123e-61
GO:BP	GO:0010557	positive regulation of macromolecule biosynthetic process	1806	2593	4.190e-61
GO:BP	GO:0008219	cell death	1433	1991	5.241e-61
GO:BP	GO:0016567	protein ubiquitination	635	768	6.842e-61
GO:BP	GO:0012501	programmed cell death	1429	1987	1.782e-60
GO:BP	GO:0051716	cellular response to stimulus	4594	7376	1.806e-60
GO:BP	GO:0009653	anatomical structure morphogenesis	1877	2713	2.144e-60
GO:BP	GO:0006915	apoptotic process	1388	1923	3.553e-60
GO:BP	GO:0032879	regulation of localization	1454	2029	4.878e-60
GO:BP	GO:0006974	DNA damage response	726	908	3.782e-58
GO:BP	GO:0044238	primary metabolic process	7310	12342	4.093e-58
GO:BP	GO:0022008	neurogenesis	1286	1771	7.569e-58
GO:BP	GO:0023057	negative regulation of signaling	1072	1435	7.610e-58
GO:BP	GO:0009968	negative regulation of signal transduction	1001	1326	1.366e-57
GO:BP	GO:0010648	negative regulation of cell communication	1072	1436	1.382e-57
GO:BP	GO:0065008	regulation of biological quality	2009	2947	1.996e-57
GO:BP	GO:0016236	macroautophagy	336	362	3.150e-57
GO:BP	GO:0080135	regulation of cellular response to stress	453	519	4.695e-57
GO:BP	GO:0050793	regulation of developmental process	1708	2457	1.601e-56
GO:BP	GO:0009889	regulation of biosynthetic process	3681	5809	1.026e-55
GO:BP	GO:0141124	intracellular signaling cassette	1366	1912	8.064e-55
GO:BP	GO:0048585	negative regulation of response to stimulus	1220	1680	1.088e-54
GO:BP	GO:0006950	response to stress	2594	3948	2.765e-54
GO:BP	GO:0007010	cytoskeleton organization	1122	1529	8.169e-54
GO:BP	GO:0007005	mitochondrion organization	387	435	1.773e-53
GO:BP	GO:0048869	cellular developmental process	2878	4438	1.811e-53
GO:BP	GO:0030154	cell differentiation	2877	4437	2.248e-53
GO:BP	GO:0060341	regulation of cellular localization	786	1013	5.061e-53
GO:BP	GO:0016072	rRNA metabolic process	256	266	2.314e-52
GO:BP	GO:0045934	negative regulation of nucleobase-containing compound metabolic process	1118	1529	2.680e-52
GO:BP	GO:0006508	proteolysis	1090	1486	4.849e-52
GO:BP	GO:0061024	membrane organization	655	821	1.178e-51
GO:BP	GO:0019637	organophosphate metabolic process	825	1077	1.453e-51
GO:BP	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	369	414	1.939e-51
GO:BP	GO:0051130	positive regulation of cellular component organization	843	1105	2.020e-51
GO:BP	GO:0010556	regulation of macromolecule biosynthetic process	3564	5644	5.811e-51
GO:BP	GO:0051248	negative regulation of protein metabolic process	555	677	1.139e-50
GO:BP	GO:0065009	regulation of molecular function	1091	1496	5.031e-50
GO:BP	GO:0051253	negative regulation of RNA metabolic process	1029	1400	1.196e-49
GO:BP	GO:0048468	cell development	1935	2876	9.615e-49
GO:BP	GO:0048699	generation of neurons	1110	1536	1.028e-47
GO:BP	GO:0006364	rRNA processing	219	225	1.463e-47
GO:BP	GO:0051247	positive regulation of protein metabolic process	788	1039	3.751e-46
GO:BP	GO:0007049	cell cycle	1185	1663	4.383e-46
GO:BP	GO:0010468	regulation of gene expression	3478	5536	5.152e-46
GO:BP	GO:0032880	regulation of protein localization	701	907	5.711e-46
GO:BP	GO:0031399	regulation of protein modification process	794	1049	6.074e-46
GO:BP	GO:0030029	actin filament-based process	646	825	1.094e-45
GO:BP	GO:0016310	phosphorylation	967	1320	2.004e-45
GO:BP	GO:0044281	small molecule metabolic process	1253	1776	2.518e-45
GO:BP	GO:0009896	positive regulation of catabolic process	455	546	3.831e-45
GO:BP	GO:0072359	circulatory system development	854	1145	4.735e-45
GO:BP	GO:0048193	Golgi vesicle transport	285	312	9.983e-45
GO:BP	GO:0031175	neuron projection development	774	1023	1.251e-44
GO:BP	GO:0016197	endosomal transport	268	290	1.542e-44
GO:BP	GO:0030182	neuron differentiation	1047	1451	2.316e-44
GO:BP	GO:0048666	neuron development	872	1177	4.989e-44
GO:BP	GO:0071840	cellular component organization or biogenesis	5077	8393	5.164e-44
GO:BP	GO:1901135	carbohydrate derivative metabolic process	745	983	2.319e-43
GO:BP	GO:0006259	DNA metabolic process	759	1005	3.161e-43
GO:BP	GO:0007507	heart development	492	605	7.292e-43
GO:BP	GO:0045892	negative regulation of DNA-templated transcription	934	1280	1.326e-42
GO:BP	GO:1902679	negative regulation of RNA biosynthetic process	943	1296	3.530e-42
GO:BP	GO:0050896	response to stimulus	5400	8999	7.766e-42
GO:BP	GO:0031344	regulation of cell projection organization	526	658	1.054e-41
GO:BP	GO:0043067	regulation of programmed cell death	1073	1506	2.004e-41
GO:BP	GO:0030036	actin cytoskeleton organization	572	729	8.302e-41
GO:BP	GO:1902532	negative regulation of intracellular signal transduction	527	662	8.333e-41
GO:BP	GO:0042981	regulation of apoptotic process	1042	1462	2.986e-40
GO:BP	GO:0000902	cell morphogenesis	745	996	8.102e-40
GO:BP	GO:0048513	animal organ development	2023	3085	1.311e-39
GO:BP	GO:0120035	regulation of plasma membrane bounded cell projection organization	511	642	1.681e-39
GO:BP	GO:0010256	endomembrane system organization	491	613	2.647e-39
GO:BP	GO:0140053	mitochondrial gene expression	166	168	2.916e-39
GO:BP	GO:0034655	nucleobase-containing compound catabolic process	437	535	6.547e-39
GO:BP	GO:0006468	protein phosphorylation	890	1227	8.285e-39
GO:BP	GO:0010506	regulation of autophagy	318	367	2.157e-38
GO:BP	GO:0090407	organophosphate biosynthetic process	492	619	1.083e-37
GO:BP	GO:0051049	regulation of transport	1123	1607	2.520e-37
GO:BP	GO:0071495	cellular response to endogenous stimulus	882	1223	7.427e-37
GO:BP	GO:0048584	positive regulation of response to stimulus	1562	2331	7.655e-37
GO:BP	GO:0018193	peptidyl-amino acid modification	535	686	9.403e-37
GO:BP	GO:0097435	supramolecular fiber organization	650	861	1.019e-36
GO:BP	GO:0061061	muscle structure development	539	693	1.921e-36
GO:BP	GO:0009719	response to endogenous stimulus	1047	1489	2.043e-36
GO:BP	GO:0007167	enzyme-linked receptor protein signaling pathway	719	970	3.994e-36
GO:BP	GO:0009967	positive regulation of signal transduction	1101	1578	4.391e-36
GO:BP	GO:0006417	regulation of translation	324	380	4.861e-36
GO:BP	GO:0051239	regulation of multicellular organismal process	1930	2956	8.509e-36
GO:BP	GO:0023052	signaling	3977	6515	1.141e-35
GO:BP	GO:0006281	DNA repair	489	621	1.700e-35
GO:BP	GO:0006913	nucleocytoplasmic transport	290	334	2.396e-35
GO:BP	GO:0051169	nuclear transport	290	334	2.396e-35
GO:BP	GO:0023056	positive regulation of signaling	1232	1796	2.903e-35
GO:BP	GO:0007154	cell communication	3987	6540	5.347e-35
GO:BP	GO:0032501	multicellular organismal process	4424	7322	1.068e-34
GO:BP	GO:0042176	regulation of protein catabolic process	314	369	1.445e-34
GO:BP	GO:0010647	positive regulation of cell communication	1228	1795	2.577e-34
GO:BP	GO:0006325	chromatin organization	659	884	2.621e-34
GO:BP	GO:0031647	regulation of protein stability	289	335	4.279e-34
GO:BP	GO:0051726	regulation of cell cycle	788	1087	4.876e-34
GO:BP	GO:0030705	cytoskeleton-dependent intracellular transport	195	209	6.834e-34
GO:BP	GO:0080134	regulation of response to stress	975	1387	1.052e-33
GO:BP	GO:0009790	embryo development	817	1135	1.424e-33
GO:BP	GO:0051129	negative regulation of cellular component organization	537	701	4.180e-33
GO:BP	GO:0006399	tRNA metabolic process	195	210	4.322e-33
GO:BP	GO:0045944	positive regulation of transcription by RNA polymerase II	891	1256	6.269e-33
GO:BP	GO:0055086	nucleobase-containing small molecule metabolic process	518	673	7.384e-33
GO:BP	GO:0006753	nucleoside phosphate metabolic process	500	646	8.648e-33
GO:BP	GO:0009987	cellular process	11205	20247	9.438e-33
GO:BP	GO:0034330	cell junction organization	622	834	2.002e-32
GO:BP	GO:0048858	cell projection morphogenesis	522	681	2.739e-32
GO:BP	GO:0006091	generation of precursor metabolites and energy	386	478	3.189e-32
GO:BP	GO:0120039	plasma membrane bounded cell projection morphogenesis	518	676	5.672e-32
GO:BP	GO:0033365	protein localization to organelle	858	1209	9.395e-32
GO:BP	GO:0022402	cell cycle process	902	1280	1.139e-31
GO:BP	GO:0031400	negative regulation of protein modification process	295	349	2.336e-31
GO:BP	GO:0030031	cell projection assembly	475	613	2.455e-31
GO:BP	GO:0034976	response to endoplasmic reticulum stress	238	270	3.002e-31
GO:BP	GO:0051640	organelle localization	479	620	4.825e-31
GO:BP	GO:0000209	protein polyubiquitination	245	280	5.196e-31
GO:BP	GO:0040007	growth	679	929	6.276e-31
GO:BP	GO:0000278	mitotic cell cycle	655	892	8.723e-31
GO:BP	GO:0016050	vesicle organization	313	376	9.791e-31
GO:BP	GO:0120031	plasma membrane bounded cell projection assembly	465	600	1.060e-30
GO:BP	GO:0016043	cellular component organization	4877	8184	1.306e-30
GO:BP	GO:0051604	protein maturation	424	539	1.538e-30
GO:BP	GO:0070848	response to growth factor	544	721	1.687e-30
GO:BP	GO:0007166	cell surface receptor signaling pathway	1824	2819	2.402e-30
GO:BP	GO:0097190	apoptotic signaling pathway	468	606	2.953e-30
GO:BP	GO:0071363	cellular response to growth factor stimulus	522	689	5.091e-30
GO:BP	GO:0048812	neuron projection morphogenesis	503	660	5.217e-30
GO:BP	GO:0010638	positive regulation of organelle organization	391	492	7.629e-30
GO:BP	GO:0010970	transport along microtubule	167	178	7.988e-30
GO:BP	GO:1901137	carbohydrate derivative biosynthetic process	459	594	8.971e-30
GO:BP	GO:0050790	regulation of catalytic activity	675	928	1.010e-29
GO:BP	GO:0141188	nucleic acid catabolic process	288	343	1.396e-29
GO:BP	GO:0007033	vacuole organization	213	239	1.567e-29
GO:BP	GO:0032543	mitochondrial translation	128	130	1.567e-29
GO:BP	GO:0034504	protein localization to nucleus	270	318	2.264e-29
GO:BP	GO:0000122	negative regulation of transcription by RNA polymerase II	680	938	3.022e-29
GO:BP	GO:0031346	positive regulation of cell projection organization	297	357	4.523e-29
GO:BP	GO:0002181	cytoplasmic translation	156	165	5.878e-29
GO:BP	GO:1903311	regulation of mRNA metabolic process	265	312	7.048e-29
GO:BP	GO:0006402	mRNA catabolic process	228	261	1.260e-28
GO:BP	GO:0051493	regulation of cytoskeleton organization	405	517	1.852e-28
GO:BP	GO:0140694	membraneless organelle assembly	346	430	2.683e-28
GO:BP	GO:1901873	regulation of post-translational protein modification	215	244	3.557e-28
GO:BP	GO:0006401	RNA catabolic process	266	315	3.931e-28
GO:BP	GO:0016241	regulation of macroautophagy	170	184	3.935e-28
GO:BP	GO:0035295	tube development	779	1101	4.500e-28
GO:BP	GO:0051650	establishment of vesicle localization	182	200	5.939e-28
GO:BP	GO:0044093	positive regulation of molecular function	642	884	6.319e-28
GO:BP	GO:0016055	Wnt signaling pathway	364	458	8.786e-28
GO:BP	GO:0051648	vesicle localization	196	219	9.654e-28
GO:BP	GO:0007264	small GTPase-mediated signal transduction	395	505	1.658e-27
GO:BP	GO:0022603	regulation of anatomical structure morphogenesis	607	831	1.827e-27
GO:BP	GO:0048667	cell morphogenesis involved in neuron differentiation	457	599	2.035e-27
GO:BP	GO:0010975	regulation of neuron projection development	355	446	2.509e-27
GO:BP	GO:1902903	regulation of supramolecular fiber organization	312	383	2.680e-27
GO:BP	GO:0009888	tissue development	1343	2032	3.001e-27
GO:BP	GO:0062197	cellular response to chemical stress	266	317	3.117e-27
GO:BP	GO:0051052	regulation of DNA metabolic process	391	500	3.383e-27
GO:BP	GO:0048646	anatomical structure formation involved in morphogenesis	837	1199	3.459e-27
GO:BP	GO:1903320	regulation of protein modification by small protein conjugation or removal	210	239	3.777e-27
GO:BP	GO:0007165	signal transduction	3633	6002	4.274e-27
GO:BP	GO:0044089	positive regulation of cellular component biogenesis	394	505	4.839e-27
GO:BP	GO:0072521	purine-containing compound metabolic process	432	563	7.649e-27
GO:BP	GO:0016049	cell growth	380	485	9.941e-27
GO:BP	GO:1901698	response to nitrogen compound	761	1080	1.522e-26
GO:BP	GO:0001701	in utero embryonic development	331	413	1.752e-26
GO:BP	GO:0008654	phospholipid biosynthetic process	222	257	2.339e-26
GO:BP	GO:0008033	tRNA processing	133	139	3.096e-26
GO:BP	GO:0045595	regulation of cell differentiation	1064	1576	3.798e-26
GO:BP	GO:0051094	positive regulation of developmental process	922	1343	3.862e-26
GO:BP	GO:0035239	tube morphogenesis	633	879	6.628e-26
GO:BP	GO:0006979	response to oxidative stress	321	400	7.224e-26
GO:BP	GO:1990778	protein localization to cell periphery	297	365	7.887e-26
GO:BP	GO:0030162	regulation of proteolysis	325	406	7.887e-26
GO:BP	GO:0006282	regulation of DNA repair	198	225	8.562e-26
GO:BP	GO:0060537	muscle tissue development	341	430	1.044e-25
GO:BP	GO:0099111	microtubule-based transport	194	220	1.567e-25
GO:BP	GO:0043009	chordate embryonic development	499	671	1.945e-25
GO:BP	GO:0006403	RNA localization	179	200	2.403e-25
GO:BP	GO:0042592	homeostatic process	1157	1736	2.906e-25
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	512	692	3.094e-25
GO:BP	GO:0014706	striated muscle tissue development	325	408	3.986e-25
GO:BP	GO:0006354	DNA-templated transcription elongation	128	134	4.981e-25
GO:BP	GO:0035966	response to topologically incorrect protein	146	157	5.941e-25
GO:BP	GO:0051174	regulation of phosphorus metabolic process	679	957	6.551e-25
GO:BP	GO:0072659	protein localization to plasma membrane	244	291	6.864e-25
GO:BP	GO:0009628	response to abiotic stimulus	795	1144	7.637e-25
GO:BP	GO:0019220	regulation of phosphate metabolic process	678	956	8.566e-25
GO:BP	GO:0043254	regulation of protein-containing complex assembly	333	421	9.739e-25
GO:BP	GO:0009117	nucleotide metabolic process	381	493	1.040e-24
GO:BP	GO:0042274	ribosomal small subunit biogenesis	103	104	1.445e-24
GO:BP	GO:0007017	microtubule-based process	704	999	1.575e-24
GO:BP	GO:1903050	regulation of proteolysis involved in protein catabolic process	204	236	2.599e-24
GO:BP	GO:0006163	purine nucleotide metabolic process	338	430	3.206e-24
GO:BP	GO:0032386	regulation of intracellular transport	225	266	5.148e-24
GO:BP	GO:0022411	cellular component disassembly	348	446	6.970e-24
GO:BP	GO:0043069	negative regulation of programmed cell death	643	905	8.234e-24
GO:BP	GO:1903047	mitotic cell cycle process	542	745	8.356e-24
GO:BP	GO:0009895	negative regulation of catabolic process	290	361	1.679e-23
GO:BP	GO:0050808	synapse organization	424	563	1.978e-23
GO:BP	GO:1903829	positive regulation of protein localization	382	499	2.221e-23
GO:BP	GO:0006338	chromatin remodeling	528	725	2.378e-23
GO:BP	GO:0050821	protein stabilization	194	224	2.412e-23
GO:BP	GO:0016482	cytosolic transport	132	141	2.563e-23
GO:BP	GO:0048738	cardiac muscle tissue development	201	234	3.319e-23
GO:BP	GO:1902533	positive regulation of intracellular signal transduction	770	1113	3.711e-23
GO:BP	GO:0005975	carbohydrate metabolic process	422	561	3.771e-23
GO:BP	GO:0006839	mitochondrial transport	160	178	3.783e-23
GO:BP	GO:0042692	muscle cell differentiation	319	405	3.931e-23
GO:BP	GO:0006457	protein folding	190	219	4.542e-23
GO:BP	GO:0007015	actin filament organization	356	461	5.597e-23
GO:BP	GO:0044092	negative regulation of molecular function	416	553	7.939e-23
GO:BP	GO:2000026	regulation of multicellular organismal development	955	1418	7.984e-23
GO:BP	GO:0008610	lipid biosynthetic process	529	729	8.195e-23
GO:BP	GO:0016477	cell migration	1024	1534	1.479e-22
GO:BP	GO:0042325	regulation of phosphorylation	592	830	1.524e-22
GO:BP	GO:0043065	positive regulation of apoptotic process	399	528	1.555e-22
GO:BP	GO:0048589	developmental growth	486	663	1.779e-22
GO:BP	GO:0051054	positive regulation of DNA metabolic process	240	291	1.878e-22
GO:BP	GO:0015980	energy derivation by oxidation of organic compounds	277	345	2.146e-22
GO:BP	GO:0032970	regulation of actin filament-based process	298	376	2.146e-22
GO:BP	GO:0034599	cellular response to oxidative stress	209	247	2.326e-22
GO:BP	GO:0001558	regulation of cell growth	318	406	2.510e-22
GO:BP	GO:0048729	tissue morphogenesis	454	614	2.893e-22
GO:BP	GO:0000956	nuclear-transcribed mRNA catabolic process	120	127	3.303e-22
GO:BP	GO:0030334	regulation of cell migration	672	960	3.476e-22
GO:BP	GO:0051168	nuclear export	152	169	4.595e-22
GO:BP	GO:0043066	negative regulation of apoptotic process	618	874	4.724e-22
GO:BP	GO:0008152	metabolic process	8044	14136	6.934e-22
GO:BP	GO:0043484	regulation of RNA splicing	165	187	8.482e-22
GO:BP	GO:0040008	regulation of growth	446	604	1.139e-21
GO:BP	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	462	629	1.172e-21
GO:BP	GO:0031929	TOR signaling	150	167	1.241e-21
GO:BP	GO:0060322	head development	574	806	1.326e-21
GO:BP	GO:0000226	microtubule cytoskeleton organization	488	670	1.356e-21
GO:BP	GO:0061136	regulation of proteasomal protein catabolic process	172	197	1.437e-21
GO:BP	GO:0038202	TORC1 signaling	100	103	2.810e-21
GO:BP	GO:0072655	establishment of protein localization to mitochondrion	116	123	2.909e-21
GO:BP	GO:0070585	protein localization to mitochondrion	123	132	3.056e-21
GO:BP	GO:0006368	transcription elongation by RNA polymerase II	112	118	3.349e-21
GO:BP	GO:0043414	macromolecule methylation	119	127	4.012e-21
GO:BP	GO:0006986	response to unfolded protein	129	140	4.391e-21
GO:BP	GO:0043068	positive regulation of programmed cell death	407	546	4.696e-21
GO:BP	GO:0045017	glycerolipid biosynthetic process	209	250	5.152e-21
GO:BP	GO:0007417	central nervous system development	730	1061	6.165e-21
GO:BP	GO:0098657	import into cell	644	922	7.065e-21
GO:BP	GO:0071559	response to transforming growth factor beta	222	269	7.434e-21
GO:BP	GO:0010563	negative regulation of phosphorus metabolic process	246	304	8.809e-21
GO:BP	GO:0045936	negative regulation of phosphate metabolic process	246	304	8.809e-21
GO:BP	GO:0098876	vesicle-mediated transport to the plasma membrane	140	155	9.299e-21
GO:BP	GO:0009451	RNA modification	154	174	1.151e-20
GO:BP	GO:0019693	ribose phosphate metabolic process	297	380	1.330e-20
GO:BP	GO:0042326	negative regulation of phosphorylation	215	260	2.052e-20
GO:BP	GO:2000145	regulation of cell motility	704	1022	2.218e-20
GO:BP	GO:0070887	cellular response to chemical stimulus	1405	2192	2.218e-20
GO:BP	GO:0001932	regulation of protein phosphorylation	553	779	2.611e-20
GO:BP	GO:0031032	actomyosin structure organization	181	212	2.732e-20
GO:BP	GO:0070201	regulation of establishment of protein localization	399	537	3.297e-20
GO:BP	GO:0001944	vasculature development	542	762	3.336e-20
GO:BP	GO:0071560	cellular response to transforming growth factor beta stimulus	216	262	3.455e-20
GO:BP	GO:0031396	regulation of protein ubiquitination	170	197	4.060e-20
GO:BP	GO:0006897	endocytosis	508	709	5.501e-20
GO:BP	GO:0007034	vacuolar transport	153	174	6.945e-20
GO:BP	GO:0099003	vesicle-mediated transport in synapse	212	257	7.064e-20
GO:BP	GO:0032984	protein-containing complex disassembly	212	257	7.064e-20
GO:BP	GO:0009259	ribonucleotide metabolic process	290	372	8.055e-20
GO:BP	GO:0060627	regulation of vesicle-mediated transport	394	531	8.907e-20
GO:BP	GO:0006644	phospholipid metabolic process	303	392	1.101e-19
GO:BP	GO:0032006	regulation of TOR signaling	132	146	1.132e-19
GO:BP	GO:2001233	regulation of apoptotic signaling pathway	295	380	1.137e-19
GO:BP	GO:0032259	methylation	197	236	1.141e-19
GO:BP	GO:0007006	mitochondrial membrane organization	109	116	1.248e-19
GO:BP	GO:0030111	regulation of Wnt signaling pathway	262	331	1.433e-19
GO:BP	GO:1903432	regulation of TORC1 signaling	93	96	1.463e-19
GO:BP	GO:0060828	regulation of canonical Wnt signaling pathway	210	255	1.596e-19
GO:BP	GO:0097193	intrinsic apoptotic signaling pathway	249	312	1.721e-19
GO:BP	GO:0009150	purine ribonucleotide metabolic process	275	351	2.315e-19
GO:BP	GO:0051656	establishment of organelle localization	367	491	2.458e-19
GO:BP	GO:0060070	canonical Wnt signaling pathway	248	311	2.520e-19
GO:BP	GO:0006400	tRNA modification	92	95	2.566e-19
GO:BP	GO:1902115	regulation of organelle assembly	195	234	2.638e-19
GO:BP	GO:0018205	peptidyl-lysine modification	127	140	3.004e-19
GO:BP	GO:0046474	glycerophospholipid biosynthetic process	178	210	3.009e-19
GO:BP	GO:0015931	nucleobase-containing compound transport	197	237	3.010e-19
GO:BP	GO:0040012	regulation of locomotion	727	1067	3.649e-19
GO:BP	GO:0036503	ERAD pathway	103	109	4.415e-19
GO:BP	GO:0045732	positive regulation of protein catabolic process	177	209	4.661e-19
GO:BP	GO:0002009	morphogenesis of an epithelium	374	503	4.814e-19
GO:BP	GO:0006626	protein targeting to mitochondrion	99	104	4.954e-19
GO:BP	GO:0007409	axonogenesis	348	463	5.150e-19
GO:BP	GO:0061564	axon development	390	528	5.266e-19
GO:BP	GO:0001933	negative regulation of protein phosphorylation	202	245	6.559e-19
GO:BP	GO:0009141	nucleoside triphosphate metabolic process	223	276	1.047e-18
GO:BP	GO:0009144	purine nucleoside triphosphate metabolic process	212	260	1.071e-18
GO:BP	GO:0009199	ribonucleoside triphosphate metabolic process	212	260	1.071e-18
GO:BP	GO:0034329	cell junction assembly	373	503	1.162e-18
GO:BP	GO:0007420	brain development	532	754	1.182e-18
GO:BP	GO:0006629	lipid metabolic process	921	1391	1.186e-18
GO:BP	GO:0016032	viral process	321	423	1.204e-18
GO:BP	GO:0006352	DNA-templated transcription initiation	177	210	1.323e-18
GO:BP	GO:0007178	cell surface receptor protein serine/threonine kinase signaling pathway	282	364	1.350e-18
GO:BP	GO:0001568	blood vessel development	518	732	1.398e-18
GO:BP	GO:0044782	cilium organization	326	431	1.494e-18
GO:BP	GO:0099173	postsynapse organization	202	246	1.641e-18
GO:BP	GO:0051236	establishment of RNA localization	143	163	2.098e-18
GO:BP	GO:0032535	regulation of cellular component size	276	356	2.792e-18
GO:BP	GO:0031401	positive regulation of protein modification process	457	637	3.704e-18
GO:BP	GO:0000422	autophagy of mitochondrion	99	105	3.815e-18
GO:BP	GO:0006892	post-Golgi vesicle-mediated transport	105	113	6.614e-18
GO:BP	GO:0060271	cilium assembly	306	403	7.685e-18
GO:BP	GO:0032784	regulation of DNA-templated transcription elongation	94	99	7.715e-18
GO:BP	GO:0050658	RNA transport	140	160	8.700e-18
GO:BP	GO:0050657	nucleic acid transport	140	160	8.700e-18
GO:BP	GO:1905037	autophagosome organization	114	125	9.524e-18
GO:BP	GO:0048870	cell motility	1156	1793	9.543e-18
GO:BP	GO:0045739	positive regulation of DNA repair	123	137	9.694e-18
GO:BP	GO:0032204	regulation of telomere maintenance	104	112	1.110e-17
GO:BP	GO:0042147	retrograde transport, endosome to Golgi	97	103	1.122e-17
GO:BP	GO:0031503	protein-containing complex localization	179	215	1.168e-17
GO:BP	GO:0032956	regulation of actin cytoskeleton organization	260	334	1.189e-17
GO:BP	GO:0061013	regulation of mRNA catabolic process	167	198	1.252e-17
GO:BP	GO:0007032	endosome organization	93	98	1.313e-17
GO:BP	GO:0099504	synaptic vesicle cycle	183	221	1.508e-17
GO:BP	GO:0060562	epithelial tube morphogenesis	261	336	1.688e-17
GO:BP	GO:0009205	purine ribonucleoside triphosphate metabolic process	205	253	1.723e-17
GO:BP	GO:1901700	response to oxygen-containing compound	1081	1669	1.962e-17
GO:BP	GO:0043487	regulation of RNA stability	163	193	2.500e-17
GO:BP	GO:0045333	cellular respiration	197	242	3.061e-17
GO:BP	GO:0051146	striated muscle cell differentiation	237	301	3.305e-17
GO:BP	GO:0000045	autophagosome assembly	108	118	4.084e-17
GO:BP	GO:0035967	cellular response to topologically incorrect protein	101	109	5.362e-17
GO:BP	GO:0006414	translational elongation	78	80	5.684e-17
GO:BP	GO:2000058	regulation of ubiquitin-dependent protein catabolic process	146	170	6.598e-17
GO:BP	GO:0010564	regulation of cell cycle process	505	720	6.671e-17
GO:BP	GO:1901699	cellular response to nitrogen compound	458	645	7.378e-17
GO:BP	GO:0035051	cardiocyte differentiation	132	151	1.054e-16
GO:BP	GO:0016358	dendrite development	196	242	1.094e-16
GO:BP	GO:0009100	glycoprotein metabolic process	282	371	1.449e-16
GO:BP	GO:0141091	transforming growth factor beta receptor superfamily signaling pathway	264	344	1.855e-16
GO:BP	GO:0043488	regulation of mRNA stability	153	181	2.414e-16
GO:BP	GO:0090092	regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	213	268	2.538e-16
GO:BP	GO:0051028	mRNA transport	116	130	3.049e-16
GO:BP	GO:0032869	cellular response to insulin stimulus	171	207	3.357e-16
GO:BP	GO:0006360	transcription by RNA polymerase I	70	71	3.518e-16
GO:BP	GO:0034243	regulation of transcription elongation by RNA polymerase II	83	87	3.944e-16
GO:BP	GO:0031669	cellular response to nutrient levels	199	248	4.260e-16
GO:BP	GO:0003007	heart morphogenesis	211	266	5.398e-16
GO:BP	GO:0055007	cardiac muscle cell differentiation	106	117	5.476e-16
GO:BP	GO:0090287	regulation of cellular response to growth factor stimulus	247	320	5.936e-16
GO:BP	GO:0044770	cell cycle phase transition	384	532	5.949e-16
GO:BP	GO:0010508	positive regulation of autophagy	138	161	7.860e-16
GO:BP	GO:0006302	double-strand break repair	246	319	8.418e-16
GO:BP	GO:0007179	transforming growth factor beta receptor signaling pathway	171	208	8.515e-16
GO:BP	GO:0022604	regulation of cell morphogenesis	197	246	9.190e-16
GO:BP	GO:0051170	import into nucleus	145	171	9.481e-16
GO:BP	GO:0009725	response to hormone	616	907	9.563e-16
GO:BP	GO:0072384	organelle transport along microtubule	85	90	1.035e-15
GO:BP	GO:0070936	protein K48-linked ubiquitination	92	99	1.043e-15
GO:BP	GO:0007030	Golgi organization	132	153	1.181e-15
GO:BP	GO:0043603	amide metabolic process	334	455	1.262e-15
GO:BP	GO:0006383	transcription by RNA polymerase III	62	62	1.344e-15
GO:BP	GO:0110053	regulation of actin filament organization	208	263	1.640e-15
GO:BP	GO:0010639	negative regulation of organelle organization	267	352	1.706e-15
GO:BP	GO:0051258	protein polymerization	222	284	1.800e-15
GO:BP	GO:0042594	response to starvation	178	219	1.809e-15
GO:BP	GO:0009892	negative regulation of metabolic process	2058	3375	2.620e-15
GO:BP	GO:0045862	positive regulation of proteolysis	177	218	2.705e-15
GO:BP	GO:0006082	organic acid metabolic process	619	915	2.830e-15
GO:BP	GO:0006661	phosphatidylinositol biosynthetic process	114	129	3.084e-15
GO:BP	GO:0043436	oxoacid metabolic process	615	909	3.446e-15
GO:BP	GO:0006650	glycerophospholipid metabolic process	238	309	3.446e-15
GO:BP	GO:0032868	response to insulin	212	270	3.595e-15
GO:BP	GO:0051050	positive regulation of transport	577	847	3.771e-15
GO:BP	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	119	136	3.771e-15
GO:BP	GO:0018105	peptidyl-serine phosphorylation	146	174	4.917e-15
GO:BP	GO:0046034	ATP metabolic process	184	229	5.130e-15
GO:BP	GO:0051348	negative regulation of transferase activity	141	167	5.384e-15
GO:BP	GO:0009267	cellular response to starvation	148	177	5.722e-15
GO:BP	GO:2000142	regulation of DNA-templated transcription initiation	78	82	6.073e-15
GO:BP	GO:0003012	muscle system process	321	438	7.327e-15
GO:BP	GO:0006606	protein import into nucleus	140	166	8.318e-15
GO:BP	GO:0018209	peptidyl-serine modification	154	186	8.571e-15
GO:BP	GO:0019752	carboxylic acid metabolic process	600	887	8.571e-15
GO:BP	GO:0006900	vesicle budding from membrane	81	86	8.885e-15
GO:BP	GO:1901701	cellular response to oxygen-containing compound	778	1182	9.013e-15
GO:BP	GO:0043434	response to peptide hormone	322	440	9.168e-15
GO:BP	GO:0050684	regulation of mRNA processing	117	134	9.540e-15
GO:BP	GO:0051301	cell division	459	658	1.023e-14
GO:BP	GO:0150115	cell-substrate junction organization	94	103	1.037e-14
GO:BP	GO:0001510	RNA methylation	77	81	1.039e-14
GO:BP	GO:0090066	regulation of anatomical structure size	360	500	1.041e-14
GO:BP	GO:0061014	positive regulation of mRNA catabolic process	97	107	1.068e-14
GO:BP	GO:1901293	nucleoside phosphate biosynthetic process	240	314	1.252e-14
GO:BP	GO:0007041	lysosomal transport	119	137	1.271e-14
GO:BP	GO:0055001	muscle cell development	162	198	1.291e-14
GO:BP	GO:1903313	positive regulation of mRNA metabolic process	124	144	1.366e-14
GO:BP	GO:0033108	mitochondrial respiratory chain complex assembly	108	122	1.411e-14
GO:BP	GO:0045597	positive regulation of cell differentiation	594	879	1.604e-14
GO:BP	GO:0048514	blood vessel morphogenesis	444	635	1.630e-14
GO:BP	GO:0042273	ribosomal large subunit biogenesis	68	70	1.662e-14
GO:BP	GO:0007517	muscle organ development	273	365	1.662e-14
GO:BP	GO:0008283	cell population proliferation	1268	2015	1.741e-14
GO:BP	GO:0051338	regulation of transferase activity	358	498	1.806e-14
GO:BP	GO:0051056	regulation of small GTPase mediated signal transduction	235	307	1.823e-14
GO:BP	GO:0051240	positive regulation of multicellular organismal process	1064	1667	1.895e-14
GO:BP	GO:0000723	telomere maintenance	138	164	1.911e-14
GO:BP	GO:0005996	monosaccharide metabolic process	197	250	2.021e-14
GO:BP	GO:0007346	regulation of mitotic cell cycle	354	492	2.098e-14
GO:BP	GO:1902905	positive regulation of supramolecular fiber organization	147	177	2.256e-14
GO:BP	GO:0071375	cellular response to peptide hormone stimulus	240	315	2.344e-14
GO:BP	GO:0050807	regulation of synapse organization	236	309	2.478e-14
GO:BP	GO:0051093	negative regulation of developmental process	621	925	2.679e-14
GO:BP	GO:0032870	cellular response to hormone stimulus	445	638	2.859e-14
GO:BP	GO:0009060	aerobic respiration	162	199	3.085e-14
GO:BP	GO:0060260	regulation of transcription initiation by RNA polymerase II	71	74	3.223e-14
GO:BP	GO:0070085	glycosylation	193	245	4.139e-14
GO:BP	GO:0008088	axo-dendritic transport	78	83	4.320e-14
GO:BP	GO:0046486	glycerolipid metabolic process	293	398	5.117e-14
GO:BP	GO:0001667	ameboidal-type cell migration	186	235	5.637e-14
GO:BP	GO:0051223	regulation of protein transport	321	442	5.661e-14
GO:BP	GO:0055002	striated muscle cell development	142	171	6.948e-14
GO:BP	GO:0006367	transcription initiation at RNA polymerase II promoter	142	171	6.948e-14
GO:BP	GO:0030522	intracellular receptor signaling pathway	279	377	7.811e-14
GO:BP	GO:0060560	developmental growth involved in morphogenesis	189	240	8.497e-14
GO:BP	GO:0003013	circulatory system process	421	602	8.552e-14
GO:BP	GO:0007249	canonical NF-kappaB signal transduction	234	308	9.213e-14
GO:BP	GO:0019725	cellular homeostasis	564	835	9.793e-14
GO:BP	GO:0051017	actin filament bundle assembly	134	160	1.056e-13
GO:BP	GO:0043086	negative regulation of catalytic activity	224	293	1.063e-13
GO:BP	GO:0050803	regulation of synapse structure or activity	239	316	1.151e-13
GO:BP	GO:0034620	cellular response to unfolded protein	86	94	1.212e-13
GO:BP	GO:1901888	regulation of cell junction assembly	204	263	1.252e-13
GO:BP	GO:0061157	mRNA destabilization	92	102	1.267e-13
GO:BP	GO:0044772	mitotic cell cycle phase transition	311	428	1.339e-13
GO:BP	GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	121	142	1.578e-13
GO:BP	GO:0003205	cardiac chamber development	140	169	1.587e-13
GO:BP	GO:0051336	regulation of hydrolase activity	262	352	1.650e-13
GO:BP	GO:0003015	heart process	197	253	1.800e-13
GO:BP	GO:0060491	regulation of cell projection assembly	164	204	1.801e-13
GO:BP	GO:0019080	viral gene expression	97	109	1.854e-13
GO:BP	GO:0009101	glycoprotein biosynthetic process	228	300	1.891e-13
GO:BP	GO:0000165	MAPK cascade	507	744	2.260e-13
GO:BP	GO:0007163	establishment or maintenance of cell polarity	184	234	2.484e-13
GO:BP	GO:0032206	positive regulation of telomere maintenance	71	75	2.651e-13
GO:BP	GO:0030490	maturation of SSU-rRNA	53	53	2.710e-13
GO:BP	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	112	130	3.034e-13
GO:BP	GO:2001242	regulation of intrinsic apoptotic signaling pathway	145	177	3.297e-13
GO:BP	GO:0007044	cell-substrate junction assembly	87	96	3.436e-13
GO:BP	GO:0043085	positive regulation of catalytic activity	389	554	3.554e-13
GO:BP	GO:0030335	positive regulation of cell migration	392	559	3.845e-13
GO:BP	GO:0120032	regulation of plasma membrane bounded cell projection assembly	162	202	3.870e-13
GO:BP	GO:0043087	regulation of GTPase activity	162	202	3.870e-13
GO:BP	GO:2000779	regulation of double-strand break repair	121	143	4.585e-13
GO:BP	GO:1903052	positive regulation of proteolysis involved in protein catabolic process	116	136	4.785e-13
GO:BP	GO:0061572	actin filament bundle organization	135	163	4.833e-13
GO:BP	GO:0040011	locomotion	813	1255	4.833e-13
GO:BP	GO:0000959	mitochondrial RNA metabolic process	52	52	4.871e-13
GO:BP	GO:0048871	multicellular organismal-level homeostasis	555	825	4.921e-13
GO:BP	GO:0048588	developmental cell growth	178	226	4.930e-13
GO:BP	GO:0006486	protein glycosylation	178	226	4.930e-13
GO:BP	GO:0043413	macromolecule glycosylation	178	226	4.930e-13
GO:BP	GO:2000144	positive regulation of DNA-templated transcription initiation	66	69	5.026e-13
GO:BP	GO:0140238	presynaptic endocytosis	80	87	5.048e-13
GO:BP	GO:0036465	synaptic vesicle recycling	86	95	5.571e-13
GO:BP	GO:0043549	regulation of kinase activity	311	431	5.866e-13
GO:BP	GO:1901875	positive regulation of post-translational protein modification	113	132	5.905e-13
GO:BP	GO:0072524	pyridine-containing compound metabolic process	139	169	5.963e-13
GO:BP	GO:0032786	positive regulation of DNA-templated transcription, elongation	57	58	6.140e-13
GO:BP	GO:0046488	phosphatidylinositol metabolic process	134	162	7.209e-13
GO:BP	GO:0050779	RNA destabilization	94	106	7.712e-13
GO:BP	GO:0070482	response to oxygen levels	255	344	8.054e-13
GO:BP	GO:1903844	regulation of cellular response to transforming growth factor beta stimulus	122	145	8.258e-13
GO:BP	GO:0032456	endocytic recycling	79	86	8.397e-13
GO:BP	GO:0032007	negative regulation of TOR signaling	65	68	8.656e-13
GO:BP	GO:1903322	positive regulation of protein modification by small protein conjugation or removal	112	131	9.175e-13
GO:BP	GO:0035148	tube formation	124	148	9.661e-13
GO:BP	GO:0033044	regulation of chromosome organization	188	242	1.037e-12
GO:BP	GO:0006413	translational initiation	109	127	1.144e-12
GO:BP	GO:0000302	response to reactive oxygen species	159	199	1.193e-12
GO:BP	GO:0019827	stem cell population maintenance	146	180	1.257e-12
GO:BP	GO:0048041	focal adhesion assembly	78	85	1.401e-12
GO:BP	GO:0060047	heart contraction	189	244	1.465e-12
GO:BP	GO:2001234	negative regulation of apoptotic signaling pathway	181	232	1.483e-12
GO:BP	GO:0031589	cell-substrate adhesion	262	356	1.483e-12
GO:BP	GO:2000781	positive regulation of double-strand break repair	84	93	1.491e-12
GO:BP	GO:0021915	neural tube development	132	160	1.628e-12
GO:BP	GO:0051960	regulation of nervous system development	326	457	1.696e-12
GO:BP	GO:0010821	regulation of mitochondrion organization	100	115	2.053e-12
GO:BP	GO:0055085	transmembrane transport	1000	1578	2.053e-12
GO:BP	GO:0016239	positive regulation of macroautophagy	80	88	2.454e-12
GO:BP	GO:0140352	export from cell	614	928	2.688e-12
GO:BP	GO:0072522	purine-containing compound biosynthetic process	197	257	2.700e-12
GO:BP	GO:0044283	small molecule biosynthetic process	410	593	2.834e-12
GO:BP	GO:0033157	regulation of intracellular protein transport	126	152	2.945e-12
GO:BP	GO:0016311	dephosphorylation	171	218	2.967e-12
GO:BP	GO:0048284	organelle fusion	135	165	2.983e-12
GO:BP	GO:0043542	endothelial cell migration	173	221	2.983e-12
GO:BP	GO:0031345	negative regulation of cell projection organization	148	184	3.086e-12
GO:BP	GO:0007029	endoplasmic reticulum organization	91	103	3.189e-12
GO:BP	GO:0033673	negative regulation of kinase activity	121	145	3.411e-12
GO:BP	GO:1905475	regulation of protein localization to membrane	154	193	3.542e-12
GO:BP	GO:0045727	positive regulation of translation	116	138	3.847e-12
GO:BP	GO:0048488	synaptic vesicle endocytosis	76	83	3.847e-12
GO:BP	GO:0031667	response to nutrient levels	358	510	3.920e-12
GO:BP	GO:0019318	hexose metabolic process	176	226	4.273e-12
GO:BP	GO:0099175	regulation of postsynapse organization	125	151	4.413e-12
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	134	164	4.429e-12
GO:BP	GO:0061077	chaperone-mediated protein folding	69	74	4.932e-12
GO:BP	GO:0007040	lysosome organization	98	113	5.078e-12
GO:BP	GO:1901800	positive regulation of proteasomal protein catabolic process	98	113	5.078e-12
GO:BP	GO:0080171	lytic vacuole organization	98	113	5.078e-12
GO:BP	GO:0042770	signal transduction in response to DNA damage	140	173	5.565e-12
GO:BP	GO:0034614	cellular response to reactive oxygen species	122	147	5.884e-12
GO:BP	GO:0006890	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	53	54	6.032e-12
GO:BP	GO:2000147	positive regulation of cell motility	405	587	6.311e-12
GO:BP	GO:0010594	regulation of endothelial cell migration	137	169	7.712e-12
GO:BP	GO:1903828	negative regulation of protein localization	168	215	8.670e-12
GO:BP	GO:0072175	epithelial tube formation	114	136	8.996e-12
GO:BP	GO:0046496	nicotinamide nucleotide metabolic process	132	162	9.848e-12
GO:BP	GO:0019362	pyridine nucleotide metabolic process	132	162	9.848e-12
GO:BP	GO:0036293	response to decreased oxygen levels	234	316	1.012e-11
GO:BP	GO:0098727	maintenance of cell number	147	184	1.012e-11
GO:BP	GO:0060606	tube closure	80	89	1.065e-11
GO:BP	GO:0045444	fat cell differentiation	185	241	1.130e-11
GO:BP	GO:0051051	negative regulation of transport	295	412	1.176e-11
GO:BP	GO:0044057	regulation of system process	383	553	1.187e-11
GO:BP	GO:0043122	regulation of canonical NF-kappaB signal transduction	215	287	1.246e-11
GO:BP	GO:0060261	positive regulation of transcription initiation by RNA polymerase II	60	63	1.319e-11
GO:BP	GO:0098732	macromolecule deacylation	56	58	1.349e-11
GO:BP	GO:0048762	mesenchymal cell differentiation	192	252	1.429e-11
GO:BP	GO:0010605	negative regulation of macromolecule metabolic process	1904	3157	1.440e-11
GO:BP	GO:0031123	RNA 3’-end processing	85	96	1.473e-11
GO:BP	GO:0051495	positive regulation of cytoskeleton organization	148	186	1.522e-11
GO:BP	GO:0060485	mesenchyme development	236	320	1.645e-11
GO:BP	GO:0032886	regulation of microtubule-based process	201	266	1.672e-11
GO:BP	GO:0001843	neural tube closure	79	88	1.726e-11
GO:BP	GO:0008286	insulin receptor signaling pathway	105	124	1.949e-11
GO:BP	GO:0045859	regulation of protein kinase activity	288	402	1.950e-11
GO:BP	GO:0042177	negative regulation of protein catabolic process	100	117	2.021e-11
GO:BP	GO:0000423	mitophagy	66	71	2.356e-11
GO:BP	GO:1903008	organelle disassembly	66	71	2.356e-11
GO:BP	GO:0007416	synapse assembly	196	259	2.498e-11
GO:BP	GO:0032940	secretion by cell	565	854	2.501e-11
GO:BP	GO:0051668	localization within membrane	607	924	2.530e-11
GO:BP	GO:0048878	chemical homeostasis	678	1043	2.614e-11
GO:BP	GO:0048638	regulation of developmental growth	229	310	2.650e-11
GO:BP	GO:0030968	endoplasmic reticulum unfolded protein response	72	79	2.876e-11
GO:BP	GO:0007007	inner mitochondrial membrane organization	45	45	2.946e-11
GO:BP	GO:0090148	membrane fission	45	45	2.946e-11
GO:BP	GO:0006903	vesicle targeting	62	66	3.175e-11
GO:BP	GO:0050770	regulation of axonogenesis	120	146	3.367e-11
GO:BP	GO:0040017	positive regulation of locomotion	412	603	3.530e-11
GO:BP	GO:0050767	regulation of neurogenesis	272	378	3.615e-11
GO:BP	GO:0030336	negative regulation of cell migration	217	292	3.710e-11
GO:BP	GO:1901874	negative regulation of post-translational protein modification	83	94	3.771e-11
GO:BP	GO:0014020	primary neural tube formation	83	94	3.771e-11
GO:BP	GO:0038127	ERBB signaling pathway	108	129	4.137e-11
GO:BP	GO:0071806	protein transmembrane transport	68	74	4.474e-11
GO:BP	GO:0001841	neural tube formation	88	101	4.481e-11
GO:BP	GO:0055006	cardiac cell development	77	86	4.527e-11
GO:BP	GO:0060048	cardiac muscle contraction	117	142	4.527e-11
GO:BP	GO:1905897	regulation of response to endoplasmic reticulum stress	77	86	4.527e-11
GO:BP	GO:0010976	positive regulation of neuron projection development	128	158	4.668e-11
GO:BP	GO:0017148	negative regulation of translation	110	132	4.742e-11
GO:BP	GO:0003279	cardiac septum development	93	108	4.803e-11
GO:BP	GO:0001525	angiogenesis	377	547	4.915e-11
GO:BP	GO:0051098	regulation of binding	165	213	4.919e-11
GO:BP	GO:0031334	positive regulation of protein-containing complex assembly	157	201	4.967e-11
GO:BP	GO:0048813	dendrite morphogenesis	119	145	4.967e-11
GO:BP	GO:0008285	negative regulation of cell population proliferation	474	706	5.587e-11
GO:BP	GO:0032968	positive regulation of transcription elongation by RNA polymerase II	49	50	5.827e-11
GO:BP	GO:0006469	negative regulation of protein kinase activity	114	138	6.055e-11
GO:BP	GO:0048872	homeostasis of number of cells	242	332	6.482e-11
GO:BP	GO:0098930	axonal transport	64	69	6.549e-11
GO:BP	GO:0043543	protein acylation	79	89	6.697e-11
GO:BP	GO:0072665	protein localization to vacuole	79	89	6.697e-11
GO:BP	GO:1901292	nucleoside phosphate catabolic process	146	185	6.718e-11
GO:BP	GO:1904951	positive regulation of establishment of protein localization	240	329	6.902e-11
GO:BP	GO:0010595	positive regulation of endothelial cell migration	92	107	7.465e-11
GO:BP	GO:0006006	glucose metabolic process	145	184	9.749e-11
GO:BP	GO:0046434	organophosphate catabolic process	186	246	1.009e-10
GO:BP	GO:0030258	lipid modification	153	196	1.009e-10
GO:BP	GO:0032388	positive regulation of intracellular transport	115	140	1.009e-10
GO:BP	GO:0032271	regulation of protein polymerization	155	199	1.009e-10
GO:BP	GO:0051090	regulation of DNA-binding transcription factor activity	235	322	1.061e-10
GO:BP	GO:1901136	carbohydrate derivative catabolic process	193	257	1.181e-10
GO:BP	GO:1904263	positive regulation of TORC1 signaling	52	54	1.222e-10
GO:BP	GO:0001666	response to hypoxia	222	302	1.248e-10
GO:BP	GO:0006635	fatty acid beta-oxidation	69	76	1.271e-10
GO:BP	GO:1901987	regulation of cell cycle phase transition	301	427	1.326e-10
GO:BP	GO:0042127	regulation of cell population proliferation	1051	1685	1.342e-10
GO:BP	GO:0099177	regulation of trans-synaptic signaling	355	514	1.353e-10
GO:BP	GO:0046822	regulation of nucleocytoplasmic transport	98	116	1.378e-10
GO:BP	GO:0048598	embryonic morphogenesis	420	620	1.392e-10
GO:BP	GO:0008016	regulation of heart contraction	158	204	1.410e-10
GO:BP	GO:0006941	striated muscle contraction	148	189	1.417e-10
GO:BP	GO:0009411	response to UV	125	155	1.475e-10
GO:BP	GO:0072523	purine-containing compound catabolic process	125	155	1.475e-10
GO:BP	GO:0006405	RNA export from nucleus	80	91	1.513e-10
GO:BP	GO:0000288	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	59	63	1.513e-10
GO:BP	GO:0003229	ventricular cardiac muscle tissue development	59	63	1.513e-10
GO:BP	GO:0042255	ribosome assembly	59	63	1.513e-10
GO:BP	GO:0045927	positive regulation of growth	192	256	1.599e-10
GO:BP	GO:0040013	negative regulation of locomotion	237	326	1.627e-10
GO:BP	GO:0045022	early endosome to late endosome transport	42	42	1.679e-10
GO:BP	GO:0072331	signal transduction by p53 class mediator	131	164	1.694e-10
GO:BP	GO:0050804	modulation of chemical synaptic transmission	354	513	1.694e-10
GO:BP	GO:0048024	regulation of mRNA splicing, via spliceosome	95	112	1.745e-10
GO:BP	GO:0009887	animal organ morphogenesis	673	1042	1.778e-10
GO:BP	GO:0098927	vesicle-mediated transport between endosomal compartments	47	48	1.779e-10
GO:BP	GO:0006458	‘de novo’ protein folding	47	48	1.779e-10
GO:BP	GO:1904262	negative regulation of TORC1 signaling	47	48	1.779e-10
GO:BP	GO:0006893	Golgi to plasma membrane transport	62	67	1.801e-10
GO:BP	GO:0016073	snRNA metabolic process	55	58	1.896e-10
GO:BP	GO:0046903	secretion	643	992	2.020e-10
GO:BP	GO:0061337	cardiac conduction	82	94	2.039e-10
GO:BP	GO:0030038	contractile actin filament bundle assembly	92	108	2.206e-10
GO:BP	GO:0043149	stress fiber assembly	92	108	2.206e-10
GO:BP	GO:1903321	negative regulation of protein modification by small protein conjugation or removal	79	90	2.388e-10
GO:BP	GO:2000146	negative regulation of cell motility	225	308	2.431e-10
GO:BP	GO:0030097	hemopoiesis	633	976	2.496e-10
GO:BP	GO:0060284	regulation of cell development	556	847	2.496e-10
GO:BP	GO:0010810	regulation of cell-substrate adhesion	166	217	2.514e-10
GO:BP	GO:0006936	muscle contraction	251	349	2.563e-10
GO:BP	GO:0030178	negative regulation of Wnt signaling pathway	136	172	2.669e-10
GO:BP	GO:0009611	response to wounding	387	568	2.725e-10
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	156	202	2.754e-10
GO:BP	GO:0002262	myeloid cell homeostasis	142	181	2.791e-10
GO:BP	GO:0032790	ribosome disassembly	41	41	2.975e-10
GO:BP	GO:0032509	endosome transport via multivesicular body sorting pathway	41	41	2.975e-10
GO:BP	GO:0009314	response to radiation	306	437	2.975e-10
GO:BP	GO:0031122	cytoplasmic microtubule organization	61	66	2.987e-10
GO:BP	GO:0090257	regulation of muscle system process	175	231	2.988e-10
GO:BP	GO:0006356	regulation of transcription by RNA polymerase I	46	47	3.101e-10
GO:BP	GO:0006984	ER-nucleus signaling pathway	46	47	3.101e-10
GO:BP	GO:0010628	positive regulation of gene expression	772	1212	3.194e-10
GO:BP	GO:0055082	intracellular chemical homeostasis	485	730	3.428e-10
GO:BP	GO:0030307	positive regulation of cell growth	129	162	3.523e-10
GO:BP	GO:0060429	epithelium development	787	1238	3.588e-10
GO:BP	GO:0003231	cardiac ventricle development	105	127	3.593e-10
GO:BP	GO:0008361	regulation of cell size	143	183	3.990e-10
GO:BP	GO:0046390	ribose phosphate biosynthetic process	143	183	3.990e-10
GO:BP	GO:1900180	regulation of protein localization to nucleus	118	146	4.053e-10
GO:BP	GO:0001503	ossification	301	430	4.546e-10
GO:BP	GO:0001838	embryonic epithelial tube formation	102	123	4.830e-10
GO:BP	GO:0031397	negative regulation of protein ubiquitination	69	77	5.243e-10
GO:BP	GO:0030488	tRNA methylation	40	40	5.341e-10
GO:BP	GO:0032200	telomere organization	148	191	5.651e-10
GO:BP	GO:0046777	protein autophosphorylation	140	179	5.686e-10
GO:BP	GO:0009201	ribonucleoside triphosphate biosynthetic process	99	119	6.459e-10
GO:BP	GO:0006643	membrane lipid metabolic process	163	214	6.804e-10
GO:BP	GO:0043547	positive regulation of GTPase activity	110	135	7.224e-10
GO:BP	GO:0090090	negative regulation of canonical Wnt signaling pathway	112	138	7.788e-10
GO:BP	GO:0031109	microtubule polymerization or depolymerization	112	138	7.788e-10
GO:BP	GO:0055013	cardiac muscle cell development	71	80	7.814e-10
GO:BP	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	89	105	8.078e-10
GO:BP	GO:0048863	stem cell differentiation	183	245	8.313e-10
GO:BP	GO:1990542	mitochondrial transmembrane transport	84	98	8.313e-10
GO:BP	GO:0046785	microtubule polymerization	84	98	8.313e-10
GO:BP	GO:0030239	myofibril assembly	68	76	8.493e-10
GO:BP	GO:0150116	regulation of cell-substrate junction organization	62	68	8.888e-10
GO:BP	GO:0043244	regulation of protein-containing complex disassembly	105	128	8.990e-10
GO:BP	GO:0006997	nucleus organization	118	147	9.256e-10
GO:BP	GO:0060996	dendritic spine development	86	101	1.027e-09
GO:BP	GO:0044843	cell cycle G1/S phase transition	173	230	1.044e-09
GO:BP	GO:0170036	import into the mitochondrion	48	50	1.068e-09
GO:BP	GO:0035601	protein deacylation	48	50	1.068e-09
GO:BP	GO:0001822	kidney development	232	322	1.068e-09
GO:BP	GO:0071985	multivesicular body sorting pathway	48	50	1.068e-09
GO:BP	GO:0009166	nucleotide catabolic process	128	162	1.094e-09
GO:BP	GO:0003206	cardiac chamber morphogenesis	102	124	1.218e-09
GO:BP	GO:0009142	nucleoside triphosphate biosynthetic process	104	127	1.343e-09
GO:BP	GO:0072001	renal system development	238	332	1.369e-09
GO:BP	GO:0051345	positive regulation of hydrolase activity	157	206	1.391e-09
GO:BP	GO:1904375	regulation of protein localization to cell periphery	119	149	1.411e-09
GO:BP	GO:0044091	membrane biogenesis	61	67	1.463e-09
GO:BP	GO:0009062	fatty acid catabolic process	90	107	1.464e-09
GO:BP	GO:0009260	ribonucleotide biosynthetic process	137	176	1.642e-09
GO:BP	GO:0045786	negative regulation of cell cycle	266	377	1.675e-09
GO:BP	GO:0019395	fatty acid oxidation	92	110	1.708e-09
GO:BP	GO:0090174	organelle membrane fusion	101	123	1.825e-09
GO:BP	GO:0042073	intraciliary transport	47	49	1.851e-09
GO:BP	GO:0062012	regulation of small molecule metabolic process	230	320	1.860e-09
GO:BP	GO:0031333	negative regulation of protein-containing complex assembly	114	142	1.884e-09
GO:BP	GO:0045596	negative regulation of cell differentiation	446	671	1.921e-09
GO:BP	GO:0032008	positive regulation of TOR signaling	66	74	2.227e-09
GO:BP	GO:1901796	regulation of signal transduction by p53 class mediator	89	106	2.243e-09
GO:BP	GO:0099536	synaptic signaling	527	807	2.662e-09
GO:BP	GO:0030177	positive regulation of Wnt signaling pathway	115	144	2.898e-09
GO:BP	GO:0051084	‘de novo’ post-translational protein folding	42	43	3.010e-09
GO:BP	GO:0030308	negative regulation of cell growth	135	174	3.333e-09
GO:BP	GO:1990138	neuron projection extension	133	171	3.346e-09
GO:BP	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	88	105	3.447e-09
GO:BP	GO:0043112	receptor metabolic process	65	73	3.618e-09
GO:BP	GO:1903051	negative regulation of proteolysis involved in protein catabolic process	65	73	3.618e-09
GO:BP	GO:0071709	membrane assembly	56	61	3.863e-09
GO:BP	GO:0061951	establishment of protein localization to plasma membrane	59	65	3.998e-09
GO:BP	GO:0051241	negative regulation of multicellular organismal process	692	1087	4.046e-09
GO:BP	GO:0006906	vesicle fusion	99	121	4.088e-09
GO:BP	GO:0007160	cell-matrix adhesion	176	237	4.121e-09
GO:BP	GO:0008154	actin polymerization or depolymerization	146	191	4.227e-09
GO:BP	GO:0006119	oxidative phosphorylation	116	146	4.347e-09
GO:BP	GO:0021537	telencephalon development	206	284	4.545e-09
GO:BP	GO:0009152	purine ribonucleotide biosynthetic process	126	161	4.736e-09
GO:BP	GO:0032787	monocarboxylic acid metabolic process	411	616	4.783e-09
GO:BP	GO:0106027	neuron projection organization	80	94	4.832e-09
GO:BP	GO:0009145	purine nucleoside triphosphate biosynthetic process	94	114	5.023e-09
GO:BP	GO:0099537	trans-synaptic signaling	510	781	5.215e-09
GO:BP	GO:0090100	positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	87	104	5.223e-09
GO:BP	GO:0006476	protein deacetylation	41	42	5.268e-09
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	233	327	5.284e-09
GO:BP	GO:0006790	sulfur compound metabolic process	221	308	5.345e-09
GO:BP	GO:0030100	regulation of endocytosis	214	297	5.500e-09
GO:BP	GO:0043038	amino acid activation	45	47	5.526e-09
GO:BP	GO:1990928	response to amino acid starvation	52	56	5.727e-09
GO:BP	GO:0086065	cell communication involved in cardiac conduction	52	56	5.727e-09
GO:BP	GO:0006289	nucleotide-excision repair	72	83	5.883e-09
GO:BP	GO:0030099	myeloid cell differentiation	305	443	6.004e-09
GO:BP	GO:0051276	chromosome organization	385	574	6.328e-09
GO:BP	GO:0044088	regulation of vacuole organization	55	60	6.328e-09
GO:BP	GO:0007004	telomere maintenance via telomerase	55	60	6.328e-09
GO:BP	GO:0099518	vesicle cytoskeletal trafficking	58	64	6.476e-09
GO:BP	GO:0007254	JNK cascade	135	175	6.479e-09
GO:BP	GO:0007224	smoothened signaling pathway	119	151	6.485e-09
GO:BP	GO:1902904	negative regulation of supramolecular fiber organization	123	157	6.635e-09
GO:BP	GO:0022900	electron transport chain	102	126	6.957e-09
GO:BP	GO:0120034	positive regulation of plasma membrane bounded cell projection assembly	93	113	7.437e-09
GO:BP	GO:0048675	axon extension	93	113	7.437e-09
GO:BP	GO:0009206	purine ribonucleoside triphosphate biosynthetic process	93	113	7.437e-09
GO:BP	GO:0022406	membrane docking	74	86	7.499e-09
GO:BP	GO:0006195	purine nucleotide catabolic process	110	138	8.481e-09
GO:BP	GO:0010212	response to ionizing radiation	112	141	8.757e-09
GO:BP	GO:0006470	protein dephosphorylation	114	144	8.988e-09
GO:BP	GO:0034101	erythrocyte homeostasis	116	147	9.173e-09
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	118	150	9.302e-09
GO:BP	GO:0090101	negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	118	150	9.302e-09
GO:BP	GO:0043039	tRNA aminoacylation	44	46	9.448e-09
GO:BP	GO:0007020	microtubule nucleation	44	46	9.448e-09
GO:BP	GO:1904356	regulation of telomere maintenance via telomere lengthening	51	55	9.516e-09
GO:BP	GO:0001952	regulation of cell-matrix adhesion	99	122	9.553e-09
GO:BP	GO:0000462	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	35	35	9.885e-09
GO:BP	GO:0000460	maturation of 5.8S rRNA	35	35	9.885e-09
GO:BP	GO:0042060	wound healing	298	433	9.888e-09
GO:BP	GO:0008015	blood circulation	350	518	1.043e-08
GO:BP	GO:0090109	regulation of cell-substrate junction assembly	57	63	1.050e-08
GO:BP	GO:0051893	regulation of focal adhesion assembly	57	63	1.050e-08
GO:BP	GO:1903522	regulation of blood circulation	187	256	1.103e-08
GO:BP	GO:0060541	respiratory system development	167	225	1.192e-08
GO:BP	GO:0022904	respiratory electron transport chain	94	115	1.211e-08
GO:BP	GO:0016052	carbohydrate catabolic process	133	173	1.271e-08
GO:BP	GO:0042982	amyloid precursor protein metabolic process	65	74	1.292e-08
GO:BP	GO:0051494	negative regulation of cytoskeleton organization	121	155	1.342e-08
GO:BP	GO:0006164	purine nucleotide biosynthetic process	146	193	1.454e-08
GO:BP	GO:0071383	cellular response to steroid hormone stimulus	159	213	1.469e-08
GO:BP	GO:0032922	circadian regulation of gene expression	62	70	1.475e-08
GO:BP	GO:0006406	mRNA export from nucleus	62	70	1.475e-08
GO:BP	GO:0007173	epidermal growth factor receptor signaling pathway	89	108	1.494e-08
GO:BP	GO:0031398	positive regulation of protein ubiquitination	89	108	1.494e-08
GO:BP	GO:0104004	cellular response to environmental stimulus	239	339	1.516e-08
GO:BP	GO:0071214	cellular response to abiotic stimulus	239	339	1.516e-08
GO:BP	GO:0098916	anterograde trans-synaptic signaling	504	775	1.523e-08
GO:BP	GO:0007268	chemical synaptic transmission	504	775	1.523e-08
GO:BP	GO:0031110	regulation of microtubule polymerization or depolymerization	82	98	1.554e-08
GO:BP	GO:0010761	fibroblast migration	50	54	1.576e-08
GO:BP	GO:0009303	rRNA transcription	39	40	1.585e-08
GO:BP	GO:0035329	hippo signaling	53	58	1.705e-08
GO:BP	GO:0006611	protein export from nucleus	56	62	1.707e-08
GO:BP	GO:0006109	regulation of carbohydrate metabolic process	134	175	1.728e-08
GO:BP	GO:0090151	establishment of protein localization to mitochondrial membrane	34	34	1.752e-08
GO:BP	GO:0072344	rescue of stalled ribosome	34	34	1.752e-08
GO:BP	GO:0034063	stress granule assembly	34	34	1.752e-08
GO:BP	GO:0030048	actin filament-based movement	108	136	1.752e-08
GO:BP	GO:0071897	DNA biosynthetic process	132	172	1.758e-08
GO:BP	GO:0110020	regulation of actomyosin structure organization	84	101	1.765e-08
GO:BP	GO:0009165	nucleotide biosynthetic process	169	229	1.923e-08
GO:BP	GO:0010833	telomere maintenance via telomere lengthening	64	73	2.031e-08
GO:BP	GO:0090263	positive regulation of canonical Wnt signaling pathway	88	107	2.222e-08
GO:BP	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	69	80	2.225e-08
GO:BP	GO:0060411	cardiac septum morphogenesis	61	69	2.343e-08
GO:BP	GO:0010977	negative regulation of neuron projection development	105	132	2.464e-08
GO:BP	GO:0001837	epithelial to mesenchymal transition	131	171	2.469e-08
GO:BP	GO:0071453	cellular response to oxygen levels	127	165	2.572e-08
GO:BP	GO:0046854	phosphatidylinositol phosphate biosynthetic process	58	65	2.607e-08
GO:BP	GO:0007155	cell adhesion	945	1530	2.616e-08
GO:BP	GO:0051646	mitochondrion localization	49	53	2.619e-08
GO:BP	GO:0034198	cellular response to amino acid starvation	49	53	2.619e-08
GO:BP	GO:0030010	establishment of cell polarity	123	159	2.634e-08
GO:BP	GO:0019058	viral life cycle	220	310	2.671e-08
GO:BP	GO:0046467	membrane lipid biosynthetic process	117	150	2.673e-08
GO:BP	GO:0060998	regulation of dendritic spine development	55	61	2.765e-08
GO:BP	GO:0006446	regulation of translational initiation	71	83	2.768e-08
GO:BP	GO:0097061	dendritic spine organization	71	83	2.768e-08
GO:BP	GO:0048008	platelet-derived growth factor receptor signaling pathway	52	57	2.781e-08
GO:BP	GO:0051651	maintenance of location in cell	155	208	2.814e-08
GO:BP	GO:0032231	regulation of actin filament bundle assembly	85	103	2.977e-08
GO:BP	GO:0051402	neuron apoptotic process	211	296	3.066e-08
GO:BP	GO:0010507	negative regulation of autophagy	78	93	3.071e-08
GO:BP	GO:0036257	multivesicular body organization	33	33	3.123e-08
GO:BP	GO:0008333	endosome to lysosome transport	63	72	3.197e-08
GO:BP	GO:0097191	extrinsic apoptotic signaling pathway	169	230	3.258e-08
GO:BP	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	80	96	3.537e-08
GO:BP	GO:0006513	protein monoubiquitination	45	48	3.724e-08
GO:BP	GO:0072583	clathrin-dependent endocytosis	45	48	3.724e-08
GO:BP	GO:0016331	morphogenesis of embryonic epithelium	118	152	3.769e-08
GO:BP	GO:1903076	regulation of protein localization to plasma membrane	91	112	3.876e-08
GO:BP	GO:0099068	postsynapse assembly	75	89	4.012e-08
GO:BP	GO:0051235	maintenance of location	161	218	4.156e-08
GO:BP	GO:0061512	protein localization to cilium	65	75	4.224e-08
GO:BP	GO:0009299	mRNA transcription	48	52	4.344e-08
GO:BP	GO:0034612	response to tumor necrosis factor	168	229	4.377e-08
GO:BP	GO:0042327	positive regulation of phosphorylation	340	506	4.448e-08
GO:BP	GO:0006754	ATP biosynthetic process	84	102	4.448e-08
GO:BP	GO:0045995	regulation of embryonic development	77	92	4.667e-08
GO:BP	GO:0006418	tRNA aminoacylation for protein translation	41	43	4.696e-08
GO:BP	GO:0000966	RNA 5’-end processing	37	38	4.807e-08
GO:BP	GO:0043500	muscle adaptation	86	105	4.883e-08
GO:BP	GO:2001252	positive regulation of chromosome organization	86	105	4.883e-08
GO:BP	GO:0000380	alternative mRNA splicing, via spliceosome	62	71	5.048e-08
GO:BP	GO:0030218	erythrocyte differentiation	107	136	5.277e-08
GO:BP	GO:0051147	regulation of muscle cell differentiation	111	142	5.360e-08
GO:BP	GO:0006898	receptor-mediated endocytosis	190	264	5.483e-08
GO:BP	GO:0099022	vesicle tethering	32	32	5.577e-08
GO:BP	GO:0036258	multivesicular body assembly	32	32	5.577e-08
GO:BP	GO:0043491	phosphatidylinositol 3-kinase/protein kinase B signal transduction	212	299	5.719e-08
GO:BP	GO:0010232	vascular transport	74	88	6.094e-08
GO:BP	GO:0150104	transport across blood-brain barrier	74	88	6.094e-08
GO:BP	GO:0014812	muscle cell migration	74	88	6.094e-08
GO:BP	GO:0051962	positive regulation of nervous system development	210	296	6.203e-08
GO:BP	GO:0042789	mRNA transcription by RNA polymerase II	44	47	6.242e-08
GO:BP	GO:0032981	mitochondrial respiratory chain complex I assembly	56	63	6.658e-08
GO:BP	GO:0006278	RNA-templated DNA biosynthetic process	56	63	6.658e-08
GO:BP	GO:0010257	NADH dehydrogenase complex assembly	56	63	6.658e-08
GO:BP	GO:0051492	regulation of stress fiber assembly	76	91	7.050e-08
GO:BP	GO:0008366	axon ensheathment	122	159	7.101e-08
GO:BP	GO:0007272	ensheathment of neurons	122	159	7.101e-08
GO:BP	GO:0055008	cardiac muscle tissue morphogenesis	53	59	7.234e-08
GO:BP	GO:0009154	purine ribonucleotide catabolic process	102	129	7.287e-08
GO:BP	GO:0030323	respiratory tube development	150	202	7.380e-08
GO:BP	GO:0043401	steroid hormone receptor signaling pathway	108	138	7.561e-08
GO:BP	GO:0005977	glycogen metabolic process	71	84	7.891e-08
GO:BP	GO:0006303	double-strand break repair via nonhomologous end joining	61	70	7.925e-08
GO:BP	GO:0017004	cytochrome complex assembly	40	42	7.987e-08
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	133	176	8.209e-08
GO:BP	GO:0045324	late endosome to vacuole transport	36	37	8.334e-08
GO:BP	GO:0050769	positive regulation of neurogenesis	178	246	8.472e-08
GO:BP	GO:0072666	establishment of protein localization to vacuole	58	66	9.352e-08
GO:BP	GO:0030155	regulation of cell adhesion	511	794	9.530e-08
GO:BP	GO:0050773	regulation of dendrite development	82	100	9.860e-08
GO:BP	GO:0043409	negative regulation of MAPK cascade	121	158	9.917e-08
GO:BP	GO:0006359	regulation of transcription by RNA polymerase III	31	31	9.945e-08
GO:BP	GO:2000736	regulation of stem cell differentiation	68	80	1.012e-07
GO:BP	GO:0036294	cellular response to decreased oxygen levels	115	149	1.047e-07
GO:BP	GO:0042149	cellular response to glucose starvation	43	46	1.047e-07
GO:BP	GO:0032210	regulation of telomere maintenance via telomerase	43	46	1.047e-07
GO:BP	GO:0034644	cellular response to UV	75	90	1.061e-07
GO:BP	GO:0046328	regulation of JNK cascade	109	140	1.073e-07
GO:BP	GO:0006887	exocytosis	249	360	1.083e-07
GO:BP	GO:0001649	osteoblast differentiation	170	234	1.124e-07
GO:BP	GO:0010717	regulation of epithelial to mesenchymal transition	86	106	1.148e-07
GO:BP	GO:0003300	cardiac muscle hypertrophy	70	83	1.204e-07
GO:BP	GO:0016925	protein sumoylation	60	69	1.245e-07
GO:BP	GO:0070534	protein K63-linked ubiquitination	60	69	1.245e-07
GO:BP	GO:0051865	protein autoubiquitination	65	76	1.280e-07
GO:BP	GO:0045926	negative regulation of growth	166	228	1.290e-07
GO:BP	GO:0010906	regulation of glucose metabolic process	79	96	1.332e-07
GO:BP	GO:0043123	positive regulation of canonical NF-kappaB signal transduction	157	214	1.342e-07
GO:BP	GO:0042552	myelination	120	157	1.377e-07
GO:BP	GO:0044042	glucan metabolic process	72	86	1.401e-07
GO:BP	GO:0016242	negative regulation of macroautophagy	35	36	1.452e-07
GO:BP	GO:0009261	ribonucleotide catabolic process	106	136	1.526e-07
GO:BP	GO:0002753	cytoplasmic pattern recognition receptor signaling pathway	131	174	1.552e-07
GO:BP	GO:0050772	positive regulation of axonogenesis	67	79	1.553e-07
GO:BP	GO:0072526	pyridine-containing compound catabolic process	83	102	1.576e-07
GO:BP	GO:0005976	polysaccharide metabolic process	83	102	1.576e-07
GO:BP	GO:1903312	negative regulation of mRNA metabolic process	83	102	1.576e-07
GO:BP	GO:0045937	positive regulation of phosphate metabolic process	370	560	1.707e-07
GO:BP	GO:0010562	positive regulation of phosphorus metabolic process	370	560	1.707e-07
GO:BP	GO:0051963	regulation of synapse assembly	125	165	1.739e-07
GO:BP	GO:0018279	protein N-linked glycosylation via asparagine	42	45	1.752e-07
GO:BP	GO:1903573	negative regulation of response to endoplasmic reticulum stress	42	45	1.752e-07
GO:BP	GO:0043408	regulation of MAPK cascade	416	637	1.862e-07
GO:BP	GO:0048511	rhythmic process	214	305	1.875e-07
GO:BP	GO:0097479	synaptic vesicle localization	51	57	1.880e-07
GO:BP	GO:0032507	maintenance of protein location in cell	51	57	1.880e-07
GO:BP	GO:0051091	positive regulation of DNA-binding transcription factor activity	145	196	1.920e-07
GO:BP	GO:0000077	DNA damage checkpoint signaling	91	114	1.947e-07
GO:BP	GO:0043393	regulation of protein binding	91	114	1.947e-07
GO:BP	GO:2000785	regulation of autophagosome assembly	45	49	1.950e-07
GO:BP	GO:0010720	positive regulation of cell development	308	458	1.984e-07
GO:BP	GO:0042063	gliogenesis	243	352	2.070e-07
GO:BP	GO:2001235	positive regulation of apoptotic signaling pathway	107	138	2.129e-07
GO:BP	GO:0032989	cellular anatomical entity morphogenesis	107	138	2.129e-07
GO:BP	GO:0009185	ribonucleoside diphosphate metabolic process	99	126	2.129e-07
GO:BP	GO:0010927	cellular component assembly involved in morphogenesis	107	138	2.129e-07
GO:BP	GO:0033059	cellular pigmentation	56	64	2.324e-07
GO:BP	GO:0031113	regulation of microtubule polymerization	56	64	2.324e-07
GO:BP	GO:0015986	proton motive force-driven ATP synthesis	66	78	2.368e-07
GO:BP	GO:0030324	lung development	146	198	2.436e-07
GO:BP	GO:0045943	positive regulation of transcription by RNA polymerase I	34	35	2.515e-07
GO:BP	GO:0016051	carbohydrate biosynthetic process	142	192	2.745e-07
GO:BP	GO:0000910	cytokinesis	142	192	2.745e-07
GO:BP	GO:0060395	SMAD protein signal transduction	68	81	2.786e-07
GO:BP	GO:0007611	learning or memory	199	282	2.868e-07
GO:BP	GO:0030900	forebrain development	286	423	2.882e-07
GO:BP	GO:0009179	purine ribonucleoside diphosphate metabolic process	92	116	2.898e-07
GO:BP	GO:0009135	purine nucleoside diphosphate metabolic process	92	116	2.898e-07
GO:BP	GO:0034440	lipid oxidation	92	116	2.898e-07
GO:BP	GO:0009225	nucleotide-sugar metabolic process	41	44	2.923e-07
GO:BP	GO:0090114	COPII-coated vesicle budding	41	44	2.923e-07
GO:BP	GO:1902414	protein localization to cell junction	94	119	2.956e-07
GO:BP	GO:1901799	negative regulation of proteasomal protein catabolic process	50	56	3.012e-07
GO:BP	GO:0042987	amyloid precursor protein catabolic process	50	56	3.012e-07
GO:BP	GO:0006487	protein N-linked glycosylation	63	74	3.020e-07
GO:BP	GO:0042776	proton motive force-driven mitochondrial ATP synthesis	58	67	3.028e-07
GO:BP	GO:0034762	regulation of transmembrane transport	298	443	3.163e-07
GO:BP	GO:0033135	regulation of peptidyl-serine phosphorylation	79	97	3.167e-07
GO:BP	GO:0016601	Rac protein signal transduction	44	48	3.189e-07
GO:BP	GO:0006479	protein methylation	44	48	3.189e-07
GO:BP	GO:0006623	protein targeting to vacuole	44	48	3.189e-07
GO:BP	GO:0008213	protein alkylation	44	48	3.189e-07
GO:BP	GO:1902459	positive regulation of stem cell population maintenance	44	48	3.189e-07
GO:BP	GO:0060173	limb development	143	194	3.450e-07
GO:BP	GO:0048736	appendage development	143	194	3.450e-07
GO:BP	GO:0009191	ribonucleoside diphosphate catabolic process	83	103	3.585e-07
GO:BP	GO:0008637	apoptotic mitochondrial changes	83	103	3.585e-07
GO:BP	GO:0001934	positive regulation of protein phosphorylation	322	483	3.615e-07
GO:BP	GO:0006520	amino acid metabolic process	208	297	3.615e-07
GO:BP	GO:0097352	autophagosome maturation	55	63	3.631e-07
GO:BP	GO:0006812	monoatomic cation transport	669	1069	3.688e-07
GO:BP	GO:0010586	miRNA metabolic process	85	106	3.753e-07
GO:BP	GO:0006901	vesicle coating	37	39	3.900e-07
GO:BP	GO:0044743	protein transmembrane import into intracellular organelle	37	39	3.900e-07
GO:BP	GO:0097581	lamellipodium organization	74	90	3.944e-07
GO:BP	GO:0050890	cognition	227	328	4.213e-07
GO:BP	GO:0009132	nucleoside diphosphate metabolic process	103	133	4.240e-07
GO:BP	GO:0061462	protein localization to lysosome	52	59	4.251e-07
GO:BP	GO:0030518	nuclear receptor-mediated steroid hormone signaling pathway	95	121	4.251e-07
GO:BP	GO:0006937	regulation of muscle contraction	124	165	4.274e-07
GO:BP	GO:0062125	regulation of mitochondrial gene expression	33	34	4.316e-07
GO:BP	GO:0048732	gland development	304	454	4.504e-07
GO:BP	GO:0003281	ventricular septum development	62	73	4.614e-07
GO:BP	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	57	66	4.702e-07
GO:BP	GO:2000059	negative regulation of ubiquitin-dependent protein catabolic process	49	55	4.807e-07
GO:BP	GO:0048489	synaptic vesicle transport	40	43	4.833e-07
GO:BP	GO:0060999	positive regulation of dendritic spine development	40	43	4.833e-07
GO:BP	GO:0072595	maintenance of protein localization in organelle	40	43	4.833e-07
GO:BP	GO:0019364	pyridine nucleotide catabolic process	80	99	4.937e-07
GO:BP	GO:0008089	anterograde axonal transport	46	51	5.179e-07
GO:BP	GO:0055010	ventricular cardiac muscle tissue morphogenesis	43	47	5.228e-07
GO:BP	GO:0032527	protein exit from endoplasmic reticulum	43	47	5.228e-07
GO:BP	GO:0047496	vesicle transport along microtubule	43	47	5.228e-07
GO:BP	GO:0014897	striated muscle hypertrophy	71	86	5.309e-07
GO:BP	GO:0140056	organelle localization by membrane tethering	64	76	5.447e-07
GO:BP	GO:0007266	Rho protein signal transduction	110	144	5.472e-07
GO:BP	GO:1903513	endoplasmic reticulum to cytosol transport	28	28	5.525e-07
GO:BP	GO:0030970	retrograde protein transport, ER to cytosol	28	28	5.525e-07
GO:BP	GO:0036010	protein localization to endosome	28	28	5.525e-07
GO:BP	GO:0055080	monoatomic cation homeostasis	395	606	5.549e-07
GO:BP	GO:0003158	endothelium development	106	138	5.722e-07
GO:BP	GO:0070252	actin-mediated cell contraction	88	111	5.766e-07
GO:BP	GO:0035265	organ growth	123	164	5.808e-07
GO:BP	GO:0008589	regulation of smoothened signaling pathway	73	89	5.821e-07
GO:BP	GO:0072329	monocarboxylic acid catabolic process	98	126	6.017e-07
GO:BP	GO:0007265	Ras protein signal transduction	96	123	6.025e-07
GO:BP	GO:0030041	actin filament polymerization	121	161	6.062e-07
GO:BP	GO:0009791	post-embryonic development	75	92	6.323e-07
GO:BP	GO:1900182	positive regulation of protein localization to nucleus	77	95	6.798e-07
GO:BP	GO:0010948	negative regulation of cell cycle process	202	289	6.993e-07
GO:BP	GO:2000036	regulation of stem cell population maintenance	61	72	7.039e-07
GO:BP	GO:0042542	response to hydrogen peroxide	79	98	7.208e-07
GO:BP	GO:0009416	response to light stimulus	223	323	7.321e-07
GO:BP	GO:0061387	regulation of extent of cell growth	81	101	7.568e-07
GO:BP	GO:0060538	skeletal muscle organ development	142	194	7.739e-07
GO:BP	GO:0009134	nucleoside diphosphate catabolic process	85	107	8.131e-07
GO:BP	GO:0055117	regulation of cardiac muscle contraction	63	75	8.288e-07
GO:BP	GO:0141193	nuclear receptor-mediated signaling pathway	131	177	8.314e-07
GO:BP	GO:0035592	establishment of protein localization to extracellular region	259	382	8.425e-07
GO:BP	GO:0050801	monoatomic ion homeostasis	400	616	8.526e-07
GO:BP	GO:0043534	blood vessel endothelial cell migration	93	119	8.573e-07
GO:BP	GO:0014896	muscle hypertrophy	72	88	8.666e-07
GO:BP	GO:0000724	double-strand break repair via homologous recombination	138	188	8.781e-07
GO:BP	GO:0035567	non-canonical Wnt signaling pathway	58	68	9.000e-07
GO:BP	GO:0009306	protein secretion	257	379	9.237e-07
GO:BP	GO:0006665	sphingolipid metabolic process	125	168	9.800e-07
GO:BP	GO:0044282	small molecule catabolic process	252	371	9.829e-07
GO:BP	GO:1904358	positive regulation of telomere maintenance via telomere lengthening	27	27	9.852e-07
GO:BP	GO:0032511	late endosome to vacuole transport via multivesicular body sorting pathway	27	27	9.852e-07
GO:BP	GO:0033119	negative regulation of RNA splicing	27	27	9.852e-07
GO:BP	GO:0001101	response to acid chemical	110	145	1.017e-06
GO:BP	GO:0000725	recombinational repair	141	193	1.031e-06
GO:BP	GO:0006942	regulation of striated muscle contraction	78	97	1.049e-06
GO:BP	GO:0090316	positive regulation of intracellular protein transport	78	97	1.049e-06
GO:BP	GO:0071456	cellular response to hypoxia	108	142	1.049e-06
GO:BP	GO:0046032	ADP catabolic process	78	97	1.049e-06
GO:BP	GO:0051222	positive regulation of protein transport	182	258	1.082e-06
GO:BP	GO:0071229	cellular response to acid chemical	80	100	1.094e-06
GO:BP	GO:0009181	purine ribonucleoside diphosphate catabolic process	80	100	1.094e-06
GO:BP	GO:0009137	purine nucleoside diphosphate catabolic process	80	100	1.094e-06
GO:BP	GO:0002011	morphogenesis of an epithelial sheet	55	64	1.128e-06
GO:BP	GO:0034446	substrate adhesion-dependent cell spreading	82	103	1.133e-06
GO:BP	GO:0006310	DNA recombination	237	347	1.156e-06
GO:BP	GO:0051896	regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	185	263	1.175e-06
GO:BP	GO:0072657	protein localization to membrane	524	827	1.183e-06
GO:BP	GO:0045445	myoblast differentiation	90	115	1.208e-06
GO:BP	GO:0061448	connective tissue development	203	292	1.209e-06
GO:BP	GO:0031023	microtubule organizing center organization	115	153	1.237e-06
GO:BP	GO:0014909	smooth muscle cell migration	62	74	1.247e-06
GO:BP	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	31	32	1.286e-06
GO:BP	GO:0071526	semaphorin-plexin signaling pathway	44	49	1.347e-06
GO:BP	GO:0006497	protein lipidation	44	49	1.347e-06
GO:BP	GO:0034248	regulation of amide metabolic process	57	67	1.379e-06
GO:BP	GO:0048639	positive regulation of developmental growth	122	164	1.390e-06
GO:BP	GO:0035196	miRNA processing	41	45	1.396e-06
GO:BP	GO:0031146	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process	41	45	1.396e-06
GO:BP	GO:0018107	peptidyl-threonine phosphorylation	64	77	1.420e-06
GO:BP	GO:0043535	regulation of blood vessel endothelial cell migration	75	93	1.452e-06
GO:BP	GO:0040029	epigenetic regulation of gene expression	207	299	1.491e-06
GO:BP	GO:0071356	cellular response to tumor necrosis factor	150	208	1.567e-06
GO:BP	GO:0007610	behavior	433	674	1.571e-06
GO:BP	GO:0007369	gastrulation	143	197	1.580e-06
GO:BP	GO:0043604	amide biosynthetic process	127	172	1.585e-06
GO:BP	GO:0062207	regulation of pattern recognition receptor signaling pathway	127	172	1.585e-06
GO:BP	GO:0006873	intracellular monoatomic ion homeostasis	349	533	1.590e-06
GO:BP	GO:0060415	muscle tissue morphogenesis	59	70	1.631e-06
GO:BP	GO:0141137	positive regulation of gene expression, epigenetic	49	56	1.666e-06
GO:BP	GO:0006473	protein acetylation	49	56	1.666e-06
GO:BP	GO:0031570	DNA integrity checkpoint signaling	95	123	1.672e-06
GO:BP	GO:0006515	protein quality control for misfolded or incompletely synthesized proteins	26	26	1.744e-06
GO:BP	GO:0044272	sulfur compound biosynthetic process	112	149	1.764e-06
GO:BP	GO:0098655	monoatomic cation transmembrane transport	552	877	1.921e-06
GO:BP	GO:0046165	alcohol biosynthetic process	108	143	1.921e-06
GO:BP	GO:0031648	protein destabilization	46	52	1.946e-06
GO:BP	GO:0007098	centrosome cycle	106	140	1.995e-06
GO:BP	GO:1902117	positive regulation of organelle assembly	72	89	2.011e-06
GO:BP	GO:0071692	protein localization to extracellular region	261	388	2.069e-06
GO:BP	GO:0030003	intracellular monoatomic cation homeostasis	343	524	2.108e-06
GO:BP	GO:0043523	regulation of neuron apoptotic process	171	242	2.108e-06
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	171	242	2.108e-06
GO:BP	GO:0006998	nuclear envelope organization	51	59	2.167e-06
GO:BP	GO:0032092	positive regulation of protein binding	43	48	2.167e-06
GO:BP	GO:0001881	receptor recycling	43	48	2.167e-06
GO:BP	GO:0043200	response to amino acid	100	131	2.192e-06
GO:BP	GO:0006096	glycolytic process	76	95	2.209e-06
GO:BP	GO:0051085	chaperone cofactor-dependent protein refolding	30	31	2.215e-06
GO:BP	GO:0019082	viral protein processing	30	31	2.215e-06
GO:BP	GO:0051259	protein complex oligomerization	189	271	2.224e-06
GO:BP	GO:1903146	regulation of autophagy of mitochondrion	40	44	2.275e-06
GO:BP	GO:0097485	neuron projection guidance	169	239	2.280e-06
GO:BP	GO:0070646	protein modification by small protein removal	113	151	2.293e-06
GO:BP	GO:0043502	regulation of muscle adaptation	65	79	2.354e-06
GO:BP	GO:0039531	regulation of cytoplasmic pattern recognition receptor signaling pathway	92	119	2.374e-06
GO:BP	GO:0046031	ADP metabolic process	82	104	2.377e-06
GO:BP	GO:1901652	response to peptide	601	962	2.404e-06
GO:BP	GO:0046902	regulation of mitochondrial membrane permeability	48	55	2.622e-06
GO:BP	GO:0019216	regulation of lipid metabolic process	219	320	2.625e-06
GO:BP	GO:0003179	heart valve morphogenesis	53	62	2.686e-06
GO:BP	GO:0043467	regulation of generation of precursor metabolites and energy	103	136	2.840e-06
GO:BP	GO:1900076	regulation of cellular response to insulin stimulus	60	72	2.840e-06
GO:BP	GO:0051881	regulation of mitochondrial membrane potential	60	72	2.840e-06
GO:BP	GO:0045598	regulation of fat cell differentiation	101	133	2.944e-06
GO:BP	GO:0007411	axon guidance	168	238	2.949e-06
GO:BP	GO:0048545	response to steroid hormone	231	340	3.057e-06
GO:BP	GO:0046364	monosaccharide biosynthetic process	73	91	3.082e-06
GO:BP	GO:0045214	sarcomere organization	45	51	3.085e-06
GO:BP	GO:1903241	U2-type prespliceosome assembly	25	25	3.090e-06
GO:BP	GO:0086064	cell communication by electrical coupling involved in cardiac conduction	25	25	3.090e-06
GO:BP	GO:0000470	maturation of LSU-rRNA	25	25	3.090e-06
GO:BP	GO:1904292	regulation of ERAD pathway	25	25	3.090e-06
GO:BP	GO:0007269	neurotransmitter secretion	112	150	3.116e-06
GO:BP	GO:0099643	signal release from synapse	112	150	3.116e-06
GO:BP	GO:0016180	snRNA processing	33	35	3.146e-06
GO:BP	GO:0000154	rRNA modification	33	35	3.146e-06
GO:BP	GO:0019068	virion assembly	33	35	3.146e-06
GO:BP	GO:0006891	intra-Golgi vesicle-mediated transport	33	35	3.146e-06
GO:BP	GO:0001764	neuron migration	137	189	3.146e-06
GO:BP	GO:0050775	positive regulation of dendrite morphogenesis	33	35	3.146e-06
GO:BP	GO:0043954	cellular component maintenance	62	75	3.153e-06
GO:BP	GO:0003170	heart valve development	62	75	3.153e-06
GO:BP	GO:0006090	pyruvate metabolic process	95	124	3.173e-06
GO:BP	GO:0045185	maintenance of protein location	55	65	3.188e-06
GO:BP	GO:0099072	regulation of postsynaptic membrane neurotransmitter receptor levels	93	121	3.243e-06
GO:BP	GO:0045861	negative regulation of proteolysis	110	147	3.243e-06
GO:BP	GO:0008064	regulation of actin polymerization or depolymerization	110	147	3.243e-06
GO:BP	GO:0048278	vesicle docking	50	58	3.323e-06
GO:BP	GO:0006664	glycolipid metabolic process	83	106	3.390e-06
GO:BP	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	42	47	3.440e-06
GO:BP	GO:0050673	epithelial cell proliferation	292	441	3.551e-06
GO:BP	GO:0034097	response to cytokine	591	947	3.629e-06
GO:BP	GO:1903214	regulation of protein targeting to mitochondrion	39	43	3.675e-06
GO:BP	GO:0086001	cardiac muscle cell action potential	66	81	3.760e-06
GO:BP	GO:0030516	regulation of axon extension	68	84	4.028e-06
GO:BP	GO:0043462	regulation of ATP-dependent activity	52	61	4.107e-06
GO:BP	GO:0001654	eye development	276	415	4.147e-06
GO:BP	GO:0018210	peptidyl-threonine modification	70	87	4.251e-06
GO:BP	GO:0050678	regulation of epithelial cell proliferation	245	364	4.312e-06
GO:BP	GO:0006836	neurotransmitter transport	151	212	4.728e-06
GO:BP	GO:1902017	regulation of cilium assembly	61	74	4.736e-06
GO:BP	GO:0042775	mitochondrial ATP synthesis coupled electron transport	78	99	4.781e-06
GO:BP	GO:0016079	synaptic vesicle exocytosis	78	99	4.781e-06
GO:BP	GO:0042773	ATP synthesis coupled electron transport	78	99	4.781e-06
GO:BP	GO:0014037	Schwann cell differentiation	44	50	4.858e-06
GO:BP	GO:0098815	modulation of excitatory postsynaptic potential	44	50	4.858e-06
GO:BP	GO:0008360	regulation of cell shape	105	140	4.881e-06
GO:BP	GO:1903533	regulation of protein targeting	63	77	5.169e-06
GO:BP	GO:0003151	outflow tract morphogenesis	63	77	5.169e-06
GO:BP	GO:0050435	amyloid-beta metabolic process	49	57	5.183e-06
GO:BP	GO:0051058	negative regulation of small GTPase mediated signal transduction	49	57	5.183e-06
GO:BP	GO:0051654	establishment of mitochondrion localization	32	34	5.304e-06
GO:BP	GO:0006734	NADH metabolic process	32	34	5.304e-06
GO:BP	GO:0042790	nucleolar large rRNA transcription by RNA polymerase I	24	24	5.465e-06
GO:BP	GO:0000466	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	24	24	5.465e-06
GO:BP	GO:0032212	positive regulation of telomere maintenance via telomerase	24	24	5.465e-06
GO:BP	GO:0060759	regulation of response to cytokine stimulus	128	176	5.503e-06
GO:BP	GO:0031124	mRNA 3’-end processing	41	46	5.525e-06
GO:BP	GO:0045667	regulation of osteoblast differentiation	99	131	5.525e-06
GO:BP	GO:0002183	cytoplasmic translational initiation	41	46	5.525e-06
GO:BP	GO:0034394	protein localization to cell surface	56	67	5.620e-06
GO:BP	GO:0002221	pattern recognition receptor signaling pathway	185	267	5.748e-06
GO:BP	GO:1902991	regulation of amyloid precursor protein catabolic process	38	42	5.968e-06
GO:BP	GO:0010662	regulation of striated muscle cell apoptotic process	38	42	5.968e-06
GO:BP	GO:0043001	Golgi to plasma membrane protein transport	38	42	5.968e-06
GO:BP	GO:0010762	regulation of fibroblast migration	35	38	5.968e-06
GO:BP	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	35	38	5.968e-06
GO:BP	GO:0003018	vascular process in circulatory system	188	272	6.074e-06
GO:BP	GO:0060997	dendritic spine morphogenesis	51	60	6.280e-06
GO:BP	GO:0008631	intrinsic apoptotic signaling pathway in response to oxidative stress	51	60	6.280e-06
GO:BP	GO:0048259	regulation of receptor-mediated endocytosis	91	119	6.284e-06
GO:BP	GO:0019083	viral transcription	46	53	6.358e-06
GO:BP	GO:0045815	transcription initiation-coupled chromatin remodeling	46	53	6.358e-06
GO:BP	GO:0002831	regulation of response to biotic stimulus	350	540	6.416e-06
GO:BP	GO:2001236	regulation of extrinsic apoptotic signaling pathway	115	156	6.447e-06
GO:BP	GO:0098662	inorganic cation transmembrane transport	535	854	6.473e-06
GO:BP	GO:0090311	regulation of protein deacetylation	28	29	6.493e-06
GO:BP	GO:0045116	protein neddylation	28	29	6.493e-06
GO:BP	GO:0071230	cellular response to amino acid stimulus	73	92	6.532e-06
GO:BP	GO:0032273	positive regulation of protein polymerization	73	92	6.532e-06
GO:BP	GO:2000278	regulation of DNA biosynthetic process	73	92	6.532e-06
GO:BP	GO:1903509	liposaccharide metabolic process	83	107	6.728e-06
GO:BP	GO:0009408	response to heat	79	101	6.771e-06
GO:BP	GO:0002027	regulation of heart rate	79	101	6.771e-06
GO:BP	GO:0007219	Notch signaling pathway	134	186	7.142e-06
GO:BP	GO:0030832	regulation of actin filament length	111	150	7.229e-06
GO:BP	GO:1903053	regulation of extracellular matrix organization	53	63	7.358e-06
GO:BP	GO:1903747	regulation of establishment of protein localization to mitochondrion	43	49	7.615e-06
GO:BP	GO:0043536	positive regulation of blood vessel endothelial cell migration	48	56	7.968e-06
GO:BP	GO:0007519	skeletal muscle tissue development	130	180	8.308e-06
GO:BP	GO:0051261	protein depolymerization	92	121	8.448e-06
GO:BP	GO:0006767	water-soluble vitamin metabolic process	55	66	8.448e-06
GO:BP	GO:0010632	regulation of epithelial cell migration	55	66	8.448e-06
GO:BP	GO:0010657	muscle cell apoptotic process	66	82	8.554e-06
GO:BP	GO:0035107	appendage morphogenesis	114	155	8.643e-06
GO:BP	GO:0035108	limb morphogenesis	114	155	8.643e-06
GO:BP	GO:0010658	striated muscle cell apoptotic process	40	45	8.793e-06
GO:BP	GO:0061001	regulation of dendritic spine morphogenesis	40	45	8.793e-06
GO:BP	GO:0060071	Wnt signaling pathway, planar cell polarity pathway	40	45	8.793e-06
GO:BP	GO:0010644	cell communication by electrical coupling	31	33	8.824e-06
GO:BP	GO:0008053	mitochondrial fusion	31	33	8.824e-06
GO:BP	GO:0048199	vesicle targeting, to, from or within Golgi	31	33	8.824e-06
GO:BP	GO:0045446	endothelial cell differentiation	88	115	8.905e-06
GO:BP	GO:0043473	pigmentation	88	115	8.905e-06
GO:BP	GO:1902369	negative regulation of RNA catabolic process	72	91	9.379e-06
GO:BP	GO:0019646	aerobic electron transport chain	72	91	9.379e-06
GO:BP	GO:1901879	regulation of protein depolymerization	72	91	9.379e-06
GO:BP	GO:0090559	regulation of membrane permeability	57	69	9.389e-06
GO:BP	GO:0002028	regulation of sodium ion transport	57	69	9.389e-06
GO:BP	GO:1905477	positive regulation of protein localization to membrane	82	106	9.432e-06
GO:BP	GO:0044804	nucleophagy	23	23	9.562e-06
GO:BP	GO:0016237	microautophagy	23	23	9.562e-06
GO:BP	GO:0000963	mitochondrial RNA processing	23	23	9.562e-06
GO:BP	GO:0050686	negative regulation of mRNA processing	23	23	9.562e-06
GO:BP	GO:0090042	tubulin deacetylation	23	23	9.562e-06
GO:BP	GO:0006739	NADP metabolic process	37	41	9.562e-06
GO:BP	GO:0010770	positive regulation of cell morphogenesis	34	37	9.710e-06
GO:BP	GO:1901524	regulation of mitophagy	34	37	9.710e-06
GO:BP	GO:0007018	microtubule-based movement	312	478	9.844e-06
GO:BP	GO:0032409	regulation of transporter activity	131	182	1.002e-05
GO:BP	GO:0035264	multicellular organism growth	117	160	1.006e-05
GO:BP	GO:1902600	proton transmembrane transport	136	190	1.045e-05
GO:BP	GO:0046395	carboxylic acid catabolic process	171	246	1.051e-05
GO:BP	GO:0016054	organic acid catabolic process	171	246	1.051e-05
GO:BP	GO:0007051	spindle organization	146	206	1.094e-05
GO:BP	GO:0001763	morphogenesis of a branching structure	146	206	1.094e-05
GO:BP	GO:0034643	establishment of mitochondrion localization, microtubule-mediated	27	28	1.105e-05
GO:BP	GO:0047497	mitochondrion transport along microtubule	27	28	1.105e-05
GO:BP	GO:0009081	branched-chain amino acid metabolic process	27	28	1.105e-05
GO:BP	GO:2000819	regulation of nucleotide-excision repair	27	28	1.105e-05
GO:BP	GO:0044380	protein localization to cytoskeleton	52	62	1.105e-05
GO:BP	GO:0010001	glial cell differentiation	182	264	1.139e-05
GO:BP	GO:0034220	monoatomic ion transmembrane transport	646	1048	1.139e-05
GO:BP	GO:0045911	positive regulation of DNA recombination	63	78	1.172e-05
GO:BP	GO:0000271	polysaccharide biosynthetic process	47	55	1.215e-05
GO:BP	GO:0086003	cardiac muscle cell contraction	65	81	1.230e-05
GO:BP	GO:0048814	regulation of dendrite morphogenesis	54	65	1.255e-05
GO:BP	GO:0009615	response to virus	273	414	1.313e-05
GO:BP	GO:0019319	hexose biosynthetic process	69	87	1.313e-05
GO:BP	GO:0150063	visual system development	276	419	1.316e-05
GO:BP	GO:0051100	negative regulation of binding	77	99	1.348e-05
GO:BP	GO:0043648	dicarboxylic acid metabolic process	77	99	1.348e-05
GO:BP	GO:0034205	amyloid-beta formation	39	44	1.392e-05
GO:BP	GO:0032101	regulation of response to external stimulus	665	1082	1.393e-05
GO:BP	GO:1905515	non-motile cilium assembly	56	68	1.393e-05
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	49	58	1.449e-05
GO:BP	GO:0048880	sensory system development	280	426	1.449e-05
GO:BP	GO:1903955	positive regulation of protein targeting to mitochondrion	30	32	1.471e-05
GO:BP	GO:0006811	monoatomic ion transport	780	1282	1.506e-05
GO:BP	GO:0060412	ventricular septum morphogenesis	36	40	1.549e-05
GO:BP	GO:0061008	hepaticobiliary system development	110	150	1.636e-05
GO:BP	GO:0006695	cholesterol biosynthetic process	51	61	1.678e-05
GO:BP	GO:1902653	secondary alcohol biosynthetic process	51	61	1.678e-05
GO:BP	GO:0051898	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	51	61	1.678e-05
GO:BP	GO:0048025	negative regulation of mRNA splicing, via spliceosome	22	22	1.697e-05
GO:BP	GO:0006390	mitochondrial transcription	22	22	1.697e-05
GO:BP	GO:0009083	branched-chain amino acid catabolic process	22	22	1.697e-05
GO:BP	GO:0140861	DNA repair-dependent chromatin remodeling	22	22	1.697e-05
GO:BP	GO:0006631	fatty acid metabolic process	264	400	1.729e-05
GO:BP	GO:0043242	negative regulation of protein-containing complex disassembly	66	83	1.848e-05
GO:BP	GO:0060419	heart growth	66	83	1.848e-05
GO:BP	GO:0051099	positive regulation of binding	80	104	1.848e-05
GO:BP	GO:0032365	intracellular lipid transport	41	47	1.872e-05
GO:BP	GO:1902116	negative regulation of organelle assembly	41	47	1.872e-05
GO:BP	GO:0050919	negative chemotaxis	41	47	1.872e-05
GO:BP	GO:0090398	cellular senescence	78	101	1.877e-05
GO:BP	GO:0048864	stem cell development	68	86	1.881e-05
GO:BP	GO:0060390	regulation of SMAD protein signal transduction	53	64	1.881e-05
GO:BP	GO:0006112	energy reserve metabolic process	76	98	1.899e-05
GO:BP	GO:0009226	nucleotide-sugar biosynthetic process	26	27	1.899e-05
GO:BP	GO:0042026	protein refolding	26	27	1.899e-05
GO:BP	GO:0007059	chromosome segregation	280	427	1.907e-05
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	157	225	1.935e-05
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	93	124	1.993e-05
GO:BP	GO:0045088	regulation of innate immune response	293	449	2.067e-05
GO:BP	GO:0014910	regulation of smooth muscle cell migration	55	67	2.069e-05
GO:BP	GO:0046890	regulation of lipid biosynthetic process	130	182	2.071e-05
GO:BP	GO:0071478	cellular response to radiation	130	182	2.071e-05
GO:BP	GO:0010038	response to metal ion	234	351	2.131e-05
GO:BP	GO:0022898	regulation of transmembrane transporter activity	123	171	2.155e-05
GO:BP	GO:0007612	learning	116	160	2.193e-05
GO:BP	GO:0046839	phospholipid dephosphorylation	38	43	2.206e-05
GO:BP	GO:0014044	Schwann cell development	38	43	2.206e-05
GO:BP	GO:0003208	cardiac ventricle morphogenesis	57	70	2.231e-05
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	171	248	2.249e-05
GO:BP	GO:0002064	epithelial cell development	153	219	2.302e-05
GO:BP	GO:0043010	camera-type eye development	241	363	2.423e-05
GO:BP	GO:1901185	negative regulation of ERBB signaling pathway	29	31	2.459e-05
GO:BP	GO:0150117	positive regulation of cell-substrate junction organization	29	31	2.459e-05
GO:BP	GO:0065002	intracellular protein transmembrane transport	29	31	2.459e-05
GO:BP	GO:0032205	negative regulation of telomere maintenance	35	39	2.484e-05
GO:BP	GO:0010665	regulation of cardiac muscle cell apoptotic process	35	39	2.484e-05
GO:BP	GO:0070979	protein K11-linked ubiquitination	35	39	2.484e-05
GO:BP	GO:0010660	regulation of muscle cell apoptotic process	61	76	2.484e-05
GO:BP	GO:1905898	positive regulation of response to endoplasmic reticulum stress	35	39	2.484e-05
GO:BP	GO:0001959	regulation of cytokine-mediated signaling pathway	119	165	2.493e-05
GO:BP	GO:0010811	positive regulation of cell-substrate adhesion	94	126	2.579e-05
GO:BP	GO:0070897	transcription preinitiation complex assembly	65	82	2.643e-05
GO:BP	GO:0006066	alcohol metabolic process	240	362	2.953e-05
GO:BP	GO:0090043	regulation of tubulin deacetylation	21	21	3.018e-05
GO:BP	GO:0070301	cellular response to hydrogen peroxide	54	66	3.079e-05
GO:BP	GO:0070129	regulation of mitochondrial translation	25	26	3.280e-05
GO:BP	GO:0033617	mitochondrial cytochrome c oxidase assembly	25	26	3.280e-05
GO:BP	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	25	26	3.280e-05
GO:BP	GO:0016126	sterol biosynthetic process	56	69	3.301e-05
GO:BP	GO:0043524	negative regulation of neuron apoptotic process	118	164	3.301e-05
GO:BP	GO:1901184	regulation of ERBB signaling pathway	56	69	3.301e-05
GO:BP	GO:0030833	regulation of actin filament polymerization	95	128	3.334e-05
GO:BP	GO:0106106	cold-induced thermogenesis	111	153	3.353e-05
GO:BP	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	80	105	3.482e-05
GO:BP	GO:0060840	artery development	80	105	3.482e-05
GO:BP	GO:1990823	response to leukemia inhibitory factor	80	105	3.482e-05
GO:BP	GO:0010659	cardiac muscle cell apoptotic process	37	42	3.517e-05
GO:BP	GO:0002244	hematopoietic progenitor cell differentiation	102	139	3.524e-05
GO:BP	GO:0030879	mammary gland development	102	139	3.524e-05
GO:BP	GO:0016485	protein processing	156	225	3.655e-05
GO:BP	GO:0043489	RNA stabilization	62	78	3.738e-05
GO:BP	GO:0048644	muscle organ morphogenesis	62	78	3.738e-05
GO:BP	GO:0002218	activation of innate immune response	205	305	3.769e-05
GO:BP	GO:0060612	adipose tissue development	49	59	3.796e-05
GO:BP	GO:0019915	lipid storage	72	93	3.803e-05
GO:BP	GO:0170062	nutrient storage	72	93	3.803e-05
GO:BP	GO:0014033	neural crest cell differentiation	72	93	3.803e-05
GO:BP	GO:0001889	liver development	107	147	3.836e-05
GO:BP	GO:0007422	peripheral nervous system development	70	90	3.836e-05
GO:BP	GO:0006094	gluconeogenesis	66	84	3.836e-05
GO:BP	GO:2000628	regulation of miRNA metabolic process	70	90	3.836e-05
GO:BP	GO:0051046	regulation of secretion	391	617	3.891e-05
GO:BP	GO:0032781	positive regulation of ATP-dependent activity	34	38	4.006e-05
GO:BP	GO:0046856	phosphatidylinositol dephosphorylation	28	30	4.106e-05
GO:BP	GO:0008535	respiratory chain complex IV assembly	28	30	4.106e-05
GO:BP	GO:1903055	positive regulation of extracellular matrix organization	28	30	4.106e-05
GO:BP	GO:0032233	positive regulation of actin filament bundle assembly	51	62	4.177e-05
GO:BP	GO:0042733	embryonic digit morphogenesis	51	62	4.177e-05
GO:BP	GO:1902882	regulation of response to oxidative stress	31	34	4.278e-05
GO:BP	GO:0032412	regulation of monoatomic ion transmembrane transporter activity	117	163	4.304e-05
GO:BP	GO:0010171	body morphogenesis	44	52	4.372e-05
GO:BP	GO:0051496	positive regulation of stress fiber assembly	44	52	4.372e-05
GO:BP	GO:0001890	placenta development	110	152	4.404e-05
GO:BP	GO:0046824	positive regulation of nucleocytoplasmic transport	53	65	4.518e-05
GO:BP	GO:0035924	cellular response to vascular endothelial growth factor stimulus	53	65	4.518e-05
GO:BP	GO:0034605	cellular response to heat	53	65	4.518e-05
GO:BP	GO:0002520	immune system development	142	203	4.521e-05
GO:BP	GO:0001501	skeletal system development	345	540	4.912e-05
GO:BP	GO:0042158	lipoprotein biosynthetic process	46	55	5.057e-05
GO:BP	GO:0033143	regulation of intracellular steroid hormone receptor signaling pathway	57	71	5.057e-05
GO:BP	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	46	55	5.057e-05
GO:BP	GO:0006260	DNA replication	191	283	5.205e-05
GO:BP	GO:0010631	epithelial cell migration	73	95	5.235e-05
GO:BP	GO:1903578	regulation of ATP metabolic process	59	74	5.235e-05
GO:BP	GO:0051788	response to misfolded protein	20	20	5.325e-05
GO:BP	GO:0006517	protein deglycosylation	20	20	5.325e-05
GO:BP	GO:2000434	regulation of protein neddylation	20	20	5.325e-05
GO:BP	GO:0042407	cristae formation	20	20	5.325e-05
GO:BP	GO:0030509	BMP signaling pathway	111	154	5.394e-05
GO:BP	GO:0046620	regulation of organ growth	69	89	5.396e-05
GO:BP	GO:0035418	protein localization to synapse	69	89	5.396e-05
GO:BP	GO:0061138	morphogenesis of a branching epithelium	133	189	5.409e-05
GO:BP	GO:0014032	neural crest cell development	63	80	5.414e-05
GO:BP	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	65	83	5.439e-05
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	65	83	5.439e-05
GO:BP	GO:0035330	regulation of hippo signaling	36	41	5.504e-05
GO:BP	GO:0000266	mitochondrial fission	36	41	5.504e-05
GO:BP	GO:0031111	negative regulation of microtubule polymerization or depolymerization	36	41	5.504e-05
GO:BP	GO:0038179	neurotrophin signaling pathway	36	41	5.504e-05
GO:BP	GO:0035994	response to muscle stretch	24	25	5.545e-05
GO:BP	GO:0140467	integrated stress response signaling	41	48	5.594e-05
GO:BP	GO:0070849	response to epidermal growth factor	41	48	5.594e-05
GO:BP	GO:0071763	nuclear membrane organization	41	48	5.594e-05
GO:BP	GO:0085029	extracellular matrix assembly	41	48	5.594e-05
GO:BP	GO:0007623	circadian rhythm	146	210	5.611e-05
GO:BP	GO:1904950	negative regulation of establishment of protein localization	95	129	5.613e-05
GO:BP	GO:0007613	memory	95	129	5.613e-05
GO:BP	GO:0048568	embryonic organ development	299	463	5.630e-05
GO:BP	GO:0042391	regulation of membrane potential	296	458	5.694e-05
GO:BP	GO:1990845	adaptive thermogenesis	121	170	5.723e-05
GO:BP	GO:0120161	regulation of cold-induced thermogenesis	109	151	5.742e-05
GO:BP	GO:0030148	sphingolipid biosynthetic process	84	112	5.747e-05
GO:BP	GO:0007267	cell-cell signaling	809	1342	6.006e-05
GO:BP	GO:1903530	regulation of secretion by cell	358	563	6.044e-05
GO:BP	GO:0033993	response to lipid	572	930	6.173e-05
GO:BP	GO:1905039	carboxylic acid transmembrane transport	107	148	6.183e-05
GO:BP	GO:1990830	cellular response to leukemia inhibitory factor	78	103	6.556e-05
GO:BP	GO:1990090	cellular response to nerve growth factor stimulus	43	51	6.608e-05
GO:BP	GO:0030330	DNA damage response, signal transduction by p53 class mediator	43	51	6.608e-05
GO:BP	GO:0051092	positive regulation of NF-kappaB transcription factor activity	89	120	6.704e-05
GO:BP	GO:1902473	regulation of protein localization to synapse	27	29	6.779e-05
GO:BP	GO:0010664	negative regulation of striated muscle cell apoptotic process	27	29	6.779e-05
GO:BP	GO:0043247	telomere maintenance in response to DNA damage	30	33	6.913e-05
GO:BP	GO:0045048	protein insertion into ER membrane	30	33	6.913e-05
GO:BP	GO:0045806	negative regulation of endocytosis	54	67	6.969e-05
GO:BP	GO:1902108	regulation of mitochondrial membrane permeability involved in apoptotic process	38	44	7.050e-05
GO:BP	GO:0098609	cell-cell adhesion	598	976	7.323e-05
GO:BP	GO:0034763	negative regulation of transmembrane transport	85	114	7.476e-05
GO:BP	GO:1901880	negative regulation of protein depolymerization	58	73	7.477e-05
GO:BP	GO:0060324	face development	45	54	7.543e-05
GO:BP	GO:0010611	regulation of cardiac muscle hypertrophy	45	54	7.543e-05
GO:BP	GO:0045661	regulation of myoblast differentiation	60	76	7.604e-05
GO:BP	GO:0001570	vasculogenesis	66	85	7.618e-05
GO:BP	GO:0002200	somatic diversification of immune receptors	62	79	7.663e-05
GO:BP	GO:0021543	pallium development	138	198	7.971e-05
GO:BP	GO:0014888	striated muscle adaptation	40	47	8.622e-05
GO:BP	GO:0021762	substantia nigra development	40	47	8.622e-05
GO:BP	GO:0048753	pigment granule organization	35	40	8.665e-05
GO:BP	GO:1903115	regulation of actin filament-based movement	35	40	8.665e-05
GO:BP	GO:1900077	negative regulation of cellular response to insulin stimulus	35	40	8.665e-05
GO:BP	GO:0033002	muscle cell proliferation	144	208	9.051e-05
GO:BP	GO:2001244	positive regulation of intrinsic apoptotic signaling pathway	49	60	9.130e-05
GO:BP	GO:1903825	organic acid transmembrane transport	109	152	9.225e-05
GO:BP	GO:0090672	telomerase RNA localization	19	19	9.346e-05
GO:BP	GO:0071025	RNA surveillance	19	19	9.346e-05
GO:BP	GO:0090671	telomerase RNA localization to Cajal body	19	19	9.346e-05
GO:BP	GO:0010968	regulation of microtubule nucleation	19	19	9.346e-05
GO:BP	GO:0055003	cardiac myofibril assembly	19	19	9.346e-05
GO:BP	GO:0090685	RNA localization to nucleus	19	19	9.346e-05
GO:BP	GO:1904505	regulation of telomere maintenance in response to DNA damage	19	19	9.346e-05
GO:BP	GO:0045945	positive regulation of transcription by RNA polymerase III	19	19	9.346e-05
GO:BP	GO:0090670	RNA localization to Cajal body	19	19	9.346e-05
GO:BP	GO:0003299	muscle hypertrophy in response to stress	23	24	9.396e-05
GO:BP	GO:0007042	lysosomal lumen acidification	23	24	9.396e-05
GO:BP	GO:0014887	cardiac muscle adaptation	23	24	9.396e-05
GO:BP	GO:0051961	negative regulation of nervous system development	102	141	9.396e-05
GO:BP	GO:0051457	maintenance of protein location in nucleus	23	24	9.396e-05
GO:BP	GO:0014898	cardiac muscle hypertrophy in response to stress	23	24	9.396e-05
GO:BP	GO:0043433	negative regulation of DNA-binding transcription factor activity	95	130	9.396e-05
GO:BP	GO:0043255	regulation of carbohydrate biosynthetic process	73	96	9.662e-05
GO:BP	GO:0043062	extracellular structure organization	217	328	9.795e-05
GO:BP	GO:0046825	regulation of protein export from nucleus	32	36	1.011e-04
GO:BP	GO:1902003	regulation of amyloid-beta formation	32	36	1.011e-04
GO:BP	GO:0007035	vacuolar acidification	32	36	1.011e-04
GO:BP	GO:1903749	positive regulation of establishment of protein localization to mitochondrion	32	36	1.011e-04
GO:BP	GO:0006099	tricarboxylic acid cycle	32	36	1.011e-04
GO:BP	GO:0048754	branching morphogenesis of an epithelial tube	112	157	1.020e-04
GO:BP	GO:1901264	carbohydrate derivative transport	69	90	1.024e-04
GO:BP	GO:0048167	regulation of synaptic plasticity	153	223	1.044e-04
GO:BP	GO:0071901	negative regulation of protein serine/threonine kinase activity	57	72	1.067e-04
GO:BP	GO:0032272	negative regulation of protein polymerization	57	72	1.067e-04
GO:BP	GO:0006970	response to osmotic stress	65	84	1.067e-04
GO:BP	GO:0031099	regeneration	140	202	1.070e-04
GO:BP	GO:0140029	exocytic process	63	81	1.077e-04
GO:BP	GO:0055017	cardiac muscle tissue growth	59	75	1.078e-04
GO:BP	GO:1905168	positive regulation of double-strand break repair via homologous recombination	37	43	1.084e-04
GO:BP	GO:0071364	cellular response to epidermal growth factor stimulus	37	43	1.084e-04
GO:BP	GO:0005978	glycogen biosynthetic process	37	43	1.084e-04
GO:BP	GO:0009250	glucan biosynthetic process	37	43	1.084e-04
GO:BP	GO:0035751	regulation of lysosomal lumen pH	29	32	1.113e-04
GO:BP	GO:0180046	GPI anchored protein biosynthesis	29	32	1.113e-04
GO:BP	GO:0006622	protein targeting to lysosome	29	32	1.113e-04
GO:BP	GO:0006505	GPI anchor metabolic process	29	32	1.113e-04
GO:BP	GO:0098901	regulation of cardiac muscle cell action potential	26	28	1.113e-04
GO:BP	GO:1901798	positive regulation of signal transduction by p53 class mediator	26	28	1.113e-04
GO:BP	GO:0170034	L-amino acid biosynthetic process	44	53	1.119e-04
GO:BP	GO:0009266	response to temperature stimulus	120	170	1.130e-04
GO:BP	GO:0002040	sprouting angiogenesis	96	132	1.154e-04
GO:BP	GO:0030198	extracellular matrix organization	216	327	1.178e-04
GO:BP	GO:0002758	innate immune response-activating signaling pathway	190	284	1.189e-04
GO:BP	GO:0098771	inorganic ion homeostasis	339	534	1.230e-04
GO:BP	GO:0001704	formation of primary germ layer	94	129	1.238e-04
GO:BP	GO:0043405	regulation of MAP kinase activity	85	115	1.278e-04
GO:BP	GO:0045089	positive regulation of innate immune response	244	374	1.293e-04
GO:BP	GO:0045229	external encapsulating structure organization	217	329	1.301e-04
GO:BP	GO:0006284	base-excision repair	39	46	1.302e-04
GO:BP	GO:0007031	peroxisome organization	34	39	1.342e-04
GO:BP	GO:0071711	basement membrane organization	34	39	1.342e-04
GO:BP	GO:0046627	negative regulation of insulin receptor signaling pathway	34	39	1.342e-04
GO:BP	GO:0034389	lipid droplet organization	34	39	1.342e-04
GO:BP	GO:0032438	melanosome organization	34	39	1.342e-04
GO:BP	GO:0032435	negative regulation of proteasomal ubiquitin-dependent protein catabolic process	34	39	1.342e-04
GO:BP	GO:0045010	actin nucleation	50	62	1.402e-04
GO:BP	GO:0042058	regulation of epidermal growth factor receptor signaling pathway	50	62	1.402e-04
GO:BP	GO:0000075	cell cycle checkpoint signaling	129	185	1.424e-04
GO:BP	GO:1901890	positive regulation of cell junction assembly	81	109	1.430e-04
GO:BP	GO:0098660	inorganic ion transmembrane transport	577	944	1.482e-04
GO:BP	GO:0071345	cellular response to cytokine stimulus	525	854	1.491e-04
GO:BP	GO:0006111	regulation of gluconeogenesis	41	49	1.503e-04
GO:BP	GO:0023061	signal release	319	501	1.514e-04
GO:BP	GO:0030032	lamellipodium assembly	56	71	1.523e-04
GO:BP	GO:0061614	miRNA transcription	60	77	1.526e-04
GO:BP	GO:0009247	glycolipid biosynthetic process	60	77	1.526e-04
GO:BP	GO:0006740	NADPH regeneration	22	23	1.593e-04
GO:BP	GO:0033962	P-body assembly	22	23	1.593e-04
GO:BP	GO:1900151	regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	22	23	1.593e-04
GO:BP	GO:0034249	negative regulation of amide metabolic process	22	23	1.593e-04
GO:BP	GO:0045879	negative regulation of smoothened signaling pathway	31	35	1.600e-04
GO:BP	GO:0046329	negative regulation of JNK cascade	31	35	1.600e-04
GO:BP	GO:0048147	negative regulation of fibroblast proliferation	31	35	1.600e-04
GO:BP	GO:1904294	positive regulation of ERAD pathway	18	18	1.628e-04
GO:BP	GO:0006743	ubiquinone metabolic process	18	18	1.628e-04
GO:BP	GO:2000641	regulation of early endosome to late endosome transport	18	18	1.628e-04
GO:BP	GO:0097494	regulation of vesicle size	18	18	1.628e-04
GO:BP	GO:0071218	cellular response to misfolded protein	18	18	1.628e-04
GO:BP	GO:0001522	pseudouridine synthesis	18	18	1.628e-04
GO:BP	GO:0032239	regulation of nucleobase-containing compound transport	18	18	1.628e-04
GO:BP	GO:0000028	ribosomal small subunit assembly	18	18	1.628e-04
GO:BP	GO:0034727	piecemeal microautophagy of the nucleus	18	18	1.628e-04
GO:BP	GO:0035278	miRNA-mediated gene silencing by inhibition of translation	18	18	1.628e-04
GO:BP	GO:0035794	positive regulation of mitochondrial membrane permeability	36	42	1.664e-04
GO:BP	GO:0097300	programmed necrotic cell death	43	52	1.666e-04
GO:BP	GO:0051224	negative regulation of protein transport	84	114	1.702e-04
GO:BP	GO:0042752	regulation of circadian rhythm	84	114	1.702e-04
GO:BP	GO:0031623	receptor internalization	98	136	1.730e-04
GO:BP	GO:0032606	type I interferon production	91	125	1.747e-04
GO:BP	GO:0032479	regulation of type I interferon production	91	125	1.747e-04
GO:BP	GO:0006506	GPI anchor biosynthetic process	28	31	1.783e-04
GO:BP	GO:0070536	protein K63-linked deubiquitination	28	31	1.783e-04
GO:BP	GO:0046685	response to arsenic-containing substance	28	31	1.783e-04
GO:BP	GO:1903846	positive regulation of cellular response to transforming growth factor beta stimulus	28	31	1.783e-04
GO:BP	GO:0016226	iron-sulfur cluster assembly	28	31	1.783e-04
GO:BP	GO:0030511	positive regulation of transforming growth factor beta receptor signaling pathway	28	31	1.783e-04
GO:BP	GO:0031163	metallo-sulfur cluster assembly	28	31	1.783e-04
GO:BP	GO:1900101	regulation of endoplasmic reticulum unfolded protein response	28	31	1.783e-04
GO:BP	GO:0034067	protein localization to Golgi apparatus	28	31	1.783e-04
GO:BP	GO:0000018	regulation of DNA recombination	103	144	1.791e-04
GO:BP	GO:0002042	cell migration involved in sprouting angiogenesis	45	55	1.805e-04
GO:BP	GO:0010882	regulation of cardiac muscle contraction by calcium ion signaling	25	27	1.824e-04
GO:BP	GO:0031365	N-terminal protein amino acid modification	25	27	1.824e-04
GO:BP	GO:0031468	nuclear membrane reassembly	25	27	1.824e-04
GO:BP	GO:0072006	nephron development	113	160	1.850e-04
GO:BP	GO:0061025	membrane fusion	131	189	1.903e-04
GO:BP	GO:0031102	neuron projection regeneration	47	58	1.925e-04
GO:BP	GO:1904062	regulation of monoatomic cation transmembrane transport	189	284	1.954e-04
GO:BP	GO:0017157	regulation of exocytosis	126	181	1.954e-04
GO:BP	GO:0010959	regulation of metal ion transport	243	374	1.981e-04
GO:BP	GO:0001824	blastocyst development	87	119	1.992e-04
GO:BP	GO:0022612	gland morphogenesis	94	130	1.993e-04
GO:BP	GO:1901342	regulation of vasculature development	198	299	2.008e-04
GO:BP	GO:0071773	cellular response to BMP stimulus	116	165	2.008e-04
GO:BP	GO:0071772	response to BMP	116	165	2.008e-04
GO:BP	GO:2001057	reactive nitrogen species metabolic process	63	82	2.052e-04
GO:BP	GO:1905508	protein localization to microtubule organizing center	33	38	2.073e-04
GO:BP	GO:1902229	regulation of intrinsic apoptotic signaling pathway in response to DNA damage	33	38	2.073e-04
GO:BP	GO:0043470	regulation of carbohydrate catabolic process	51	64	2.077e-04
GO:BP	GO:1903078	positive regulation of protein localization to plasma membrane	51	64	2.077e-04
GO:BP	GO:0008643	carbohydrate transport	99	138	2.084e-04
GO:BP	GO:1904377	positive regulation of protein localization to cell periphery	59	76	2.122e-04
GO:BP	GO:1902893	regulation of miRNA transcription	59	76	2.122e-04
GO:BP	GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	57	73	2.137e-04
GO:BP	GO:0016444	somatic cell DNA recombination	57	73	2.137e-04
GO:BP	GO:0072073	kidney epithelium development	109	154	2.178e-04
GO:BP	GO:0050679	positive regulation of epithelial cell proliferation	140	204	2.214e-04
GO:BP	GO:0034314	Arp2/3 complex-mediated actin nucleation	40	48	2.224e-04
GO:BP	GO:0060443	mammary gland morphogenesis	40	48	2.224e-04
GO:BP	GO:0061383	trabecula morphogenesis	40	48	2.224e-04
GO:BP	GO:0021987	cerebral cortex development	95	132	2.436e-04
GO:BP	GO:0006120	mitochondrial electron transport, NADH to ubiquinone	42	51	2.471e-04
GO:BP	GO:0060914	heart formation	30	34	2.511e-04
GO:BP	GO:0086004	regulation of cardiac muscle cell contraction	30	34	2.511e-04
GO:BP	GO:0034405	response to fluid shear stress	30	34	2.511e-04
GO:BP	GO:0140058	neuron projection arborization	30	34	2.511e-04
GO:BP	GO:2000008	regulation of protein localization to cell surface	35	41	2.548e-04
GO:BP	GO:0014074	response to purine-containing compound	105	148	2.575e-04
GO:BP	GO:0044839	cell cycle G2/M phase transition	110	156	2.589e-04
GO:BP	GO:1902652	secondary alcohol metabolic process	110	156	2.589e-04
GO:BP	GO:0001659	temperature homeostasis	128	185	2.629e-04
GO:BP	GO:0050771	negative regulation of axonogenesis	44	54	2.661e-04
GO:BP	GO:0035493	SNARE complex assembly	21	22	2.666e-04
GO:BP	GO:0034472	snRNA 3’-end processing	21	22	2.666e-04
GO:BP	GO:0061709	reticulophagy	21	22	2.666e-04
GO:BP	GO:0021756	striatum development	21	22	2.666e-04
GO:BP	GO:0035050	embryonic heart tube development	66	87	2.666e-04
GO:BP	GO:0097502	mannosylation	21	22	2.666e-04
GO:BP	GO:0044794	positive regulation by host of viral process	21	22	2.666e-04
GO:BP	GO:0090130	tissue migration	77	104	2.712e-04
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	64	84	2.763e-04
GO:BP	GO:1900542	regulation of purine nucleotide metabolic process	64	84	2.763e-04
GO:BP	GO:0048010	vascular endothelial growth factor receptor signaling pathway	46	57	2.797e-04
GO:BP	GO:0099084	postsynaptic specialization organization	46	57	2.797e-04
GO:BP	GO:0001954	positive regulation of cell-matrix adhesion	46	57	2.797e-04
GO:BP	GO:0014743	regulation of muscle hypertrophy	46	57	2.797e-04
GO:BP	GO:0031098	stress-activated protein kinase signaling cascade	46	57	2.797e-04
GO:BP	GO:0035113	embryonic appendage morphogenesis	91	126	2.805e-04
GO:BP	GO:0030326	embryonic limb morphogenesis	91	126	2.805e-04
GO:BP	GO:0036507	protein demannosylation	17	17	2.834e-04
GO:BP	GO:0036508	protein alpha-1,2-demannosylation	17	17	2.834e-04
GO:BP	GO:0046209	nitric oxide metabolic process	62	81	2.834e-04
GO:BP	GO:0006415	translational termination	17	17	2.834e-04
GO:BP	GO:0060382	regulation of DNA strand elongation	17	17	2.834e-04
GO:BP	GO:0032510	endosome to lysosome transport via multivesicular body sorting pathway	17	17	2.834e-04
GO:BP	GO:0010649	regulation of cell communication by electrical coupling	17	17	2.834e-04
GO:BP	GO:0006895	Golgi to endosome transport	17	17	2.834e-04
GO:BP	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	27	30	2.837e-04
GO:BP	GO:0035891	exit from host cell	27	30	2.837e-04
GO:BP	GO:1902176	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	27	30	2.837e-04
GO:BP	GO:0010765	positive regulation of sodium ion transport	27	30	2.837e-04
GO:BP	GO:0019076	viral release from host cell	27	30	2.837e-04
GO:BP	GO:0060420	regulation of heart growth	48	60	2.886e-04
GO:BP	GO:0050768	negative regulation of neurogenesis	96	134	2.909e-04
GO:BP	GO:0021782	glial cell development	96	134	2.909e-04
GO:BP	GO:0034219	carbohydrate transmembrane transport	96	134	2.909e-04
GO:BP	GO:2000300	regulation of synaptic vesicle exocytosis	37	44	2.930e-04
GO:BP	GO:0042398	modified amino acid biosynthetic process	37	44	2.930e-04
GO:BP	GO:0010907	positive regulation of glucose metabolic process	37	44	2.930e-04
GO:BP	GO:0033674	positive regulation of kinase activity	170	254	2.932e-04
GO:BP	GO:0046755	viral budding	24	26	2.950e-04
GO:BP	GO:0048207	vesicle targeting, rough ER to cis-Golgi	24	26	2.950e-04
GO:BP	GO:0048208	COPII vesicle coating	24	26	2.950e-04
GO:BP	GO:0042180	ketone metabolic process	145	213	2.950e-04
GO:BP	GO:0051894	positive regulation of focal adhesion assembly	24	26	2.950e-04
GO:BP	GO:0034453	microtubule anchoring	24	26	2.950e-04
GO:BP	GO:0010667	negative regulation of cardiac muscle cell apoptotic process	24	26	2.950e-04
GO:BP	GO:0018345	protein palmitoylation	24	26	2.950e-04
GO:BP	GO:0031167	rRNA methylation	24	26	2.950e-04
GO:BP	GO:0033138	positive regulation of peptidyl-serine phosphorylation	52	66	2.975e-04
GO:BP	GO:0090132	epithelium migration	73	98	2.978e-04
GO:BP	GO:0016445	somatic diversification of immunoglobulins	54	69	2.981e-04
GO:BP	GO:0042221	response to chemical	2243	3909	3.022e-04
GO:BP	GO:0007423	sensory organ development	389	624	3.072e-04
GO:BP	GO:0019079	viral genome replication	94	131	3.122e-04
GO:BP	GO:0030001	metal ion transport	539	883	3.132e-04
GO:BP	GO:2000765	regulation of cytoplasmic translation	32	37	3.162e-04
GO:BP	GO:0071539	protein localization to centrosome	32	37	3.162e-04
GO:BP	GO:0003161	cardiac conduction system development	32	37	3.162e-04
GO:BP	GO:0043269	regulation of monoatomic ion transport	288	452	3.244e-04
GO:BP	GO:0010656	negative regulation of muscle cell apoptotic process	39	47	3.280e-04
GO:BP	GO:0045216	cell-cell junction organization	146	215	3.337e-04
GO:BP	GO:0034765	regulation of monoatomic ion transmembrane transport	210	321	3.491e-04
GO:BP	GO:2000377	regulation of reactive oxygen species metabolic process	102	144	3.549e-04
GO:BP	GO:0044788	modulation by host of viral process	41	50	3.596e-04
GO:BP	GO:0051489	regulation of filopodium assembly	41	50	3.596e-04
GO:BP	GO:0008593	regulation of Notch signaling pathway	74	100	3.826e-04
GO:BP	GO:0051588	regulation of neurotransmitter transport	74	100	3.826e-04
GO:BP	GO:0045765	regulation of angiogenesis	193	293	3.839e-04
GO:BP	GO:1902686	mitochondrial outer membrane permeabilization involved in programmed cell death	34	40	3.843e-04
GO:BP	GO:0051403	stress-activated MAPK cascade	43	53	3.843e-04
GO:BP	GO:1990089	response to nerve growth factor	43	53	3.843e-04
GO:BP	GO:0032366	intracellular sterol transport	29	33	3.899e-04
GO:BP	GO:2000463	positive regulation of excitatory postsynaptic potential	29	33	3.899e-04
GO:BP	GO:0015749	monosaccharide transmembrane transport	88	122	3.930e-04
GO:BP	GO:0071470	cellular response to osmotic stress	45	56	4.029e-04
GO:BP	GO:0051298	centrosome duplication	57	74	4.122e-04
GO:BP	GO:0008645	hexose transmembrane transport	86	119	4.246e-04
GO:BP	GO:0002682	regulation of immune system process	936	1581	4.421e-04
GO:BP	GO:1902175	regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	36	43	4.444e-04
GO:BP	GO:1901661	quinone metabolic process	20	21	4.470e-04
GO:BP	GO:0035268	protein mannosylation	20	21	4.470e-04
GO:BP	GO:0071786	endoplasmic reticulum tubular network organization	20	21	4.470e-04
GO:BP	GO:0010881	regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion	20	21	4.470e-04
GO:BP	GO:0018394	peptidyl-lysine acetylation	20	21	4.470e-04
GO:BP	GO:0007026	negative regulation of microtubule depolymerization	26	29	4.546e-04
GO:BP	GO:0009649	entrainment of circadian clock	26	29	4.546e-04
GO:BP	GO:0034315	regulation of Arp2/3 complex-mediated actin nucleation	26	29	4.546e-04
GO:BP	GO:0090140	regulation of mitochondrial fission	26	29	4.546e-04
GO:BP	GO:1903421	regulation of synaptic vesicle recycling	26	29	4.546e-04
GO:BP	GO:1902683	regulation of receptor localization to synapse	26	29	4.546e-04
GO:BP	GO:1904659	D-glucose transmembrane transport	84	116	4.552e-04
GO:BP	GO:0001892	embryonic placenta development	66	88	4.743e-04
GO:BP	GO:0035020	regulation of Rac protein signal transduction	23	25	4.879e-04
GO:BP	GO:0060155	platelet dense granule organization	23	25	4.879e-04
GO:BP	GO:0044090	positive regulation of vacuole organization	23	25	4.879e-04
GO:BP	GO:0070316	regulation of G0 to G1 transition	31	36	4.922e-04
GO:BP	GO:0003254	regulation of membrane depolarization	38	46	4.922e-04
GO:BP	GO:1905710	positive regulation of membrane permeability	38	46	4.922e-04
GO:BP	GO:1902745	positive regulation of lamellipodium organization	31	36	4.922e-04
GO:BP	GO:0006779	porphyrin-containing compound biosynthetic process	31	36	4.922e-04
GO:BP	GO:0033014	tetrapyrrole biosynthetic process	31	36	4.922e-04
GO:BP	GO:0016579	protein deubiquitination	94	132	4.922e-04
GO:BP	GO:1900102	negative regulation of endoplasmic reticulum unfolded protein response	16	16	4.924e-04
GO:BP	GO:0051153	regulation of striated muscle cell differentiation	64	85	4.924e-04
GO:BP	GO:0030242	autophagy of peroxisome	16	16	4.924e-04
GO:BP	GO:0000463	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	16	16	4.924e-04
GO:BP	GO:1901663	quinone biosynthetic process	16	16	4.924e-04
GO:BP	GO:0034497	protein localization to phagophore assembly site	16	16	4.924e-04
GO:BP	GO:0043328	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	16	16	4.924e-04
GO:BP	GO:2000232	regulation of rRNA processing	16	16	4.924e-04
GO:BP	GO:0099116	tRNA 5’-end processing	16	16	4.924e-04
GO:BP	GO:0060546	negative regulation of necroptotic process	16	16	4.924e-04
GO:BP	GO:0000479	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	16	16	4.924e-04
GO:BP	GO:0006140	regulation of nucleotide metabolic process	64	85	4.924e-04
GO:BP	GO:1900034	regulation of cellular response to heat	16	16	4.924e-04
GO:BP	GO:1903358	regulation of Golgi organization	16	16	4.924e-04
GO:BP	GO:0006744	ubiquinone biosynthetic process	16	16	4.924e-04
GO:BP	GO:0045785	positive regulation of cell adhesion	308	488	5.002e-04
GO:BP	GO:0071396	cellular response to lipid	381	613	5.104e-04
GO:BP	GO:0032387	negative regulation of intracellular transport	40	49	5.275e-04
GO:BP	GO:0051205	protein insertion into membrane	40	49	5.275e-04
GO:BP	GO:0030521	androgen receptor signaling pathway	40	49	5.275e-04
GO:BP	GO:0002833	positive regulation of response to biotic stimulus	256	400	5.292e-04
GO:BP	GO:0097120	receptor localization to synapse	60	79	5.337e-04
GO:BP	GO:1902373	negative regulation of mRNA catabolic process	60	79	5.337e-04
GO:BP	GO:0008203	cholesterol metabolic process	102	145	5.365e-04
GO:BP	GO:0062013	positive regulation of small molecule metabolic process	102	145	5.365e-04
GO:BP	GO:0045197	establishment or maintenance of epithelial cell apical/basal polarity	42	52	5.580e-04
GO:BP	GO:0006672	ceramide metabolic process	78	107	5.584e-04
GO:BP	GO:0038066	p38MAPK cascade	44	55	5.803e-04
GO:BP	GO:0060323	head morphogenesis	33	39	5.811e-04
GO:BP	GO:0007616	long-term memory	33	39	5.811e-04
GO:BP	GO:0090049	regulation of cell migration involved in sprouting angiogenesis	33	39	5.811e-04
GO:BP	GO:0043506	regulation of JUN kinase activity	33	39	5.811e-04
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	54	70	5.823e-04
GO:BP	GO:0045669	positive regulation of osteoblast differentiation	54	70	5.823e-04
GO:BP	GO:0045600	positive regulation of fat cell differentiation	52	67	5.923e-04
GO:BP	GO:0046626	regulation of insulin receptor signaling pathway	52	67	5.923e-04
GO:BP	GO:0016447	somatic recombination of immunoglobulin gene segments	50	64	5.976e-04
GO:BP	GO:0042306	regulation of protein import into nucleus	48	61	5.976e-04
GO:BP	GO:0006783	heme biosynthetic process	28	32	6.069e-04
GO:BP	GO:0070570	regulation of neuron projection regeneration	28	32	6.069e-04
GO:BP	GO:0062098	regulation of programmed necrotic cell death	28	32	6.069e-04
GO:BP	GO:0086019	cell-cell signaling involved in cardiac conduction	28	32	6.069e-04
GO:BP	GO:0090504	epiboly	35	42	6.617e-04
GO:BP	GO:1904861	excitatory synapse assembly	35	42	6.617e-04
GO:BP	GO:0072594	establishment of protein localization to organelle	408	661	6.737e-04
GO:BP	GO:0051225	spindle assembly	96	136	6.949e-04
GO:BP	GO:0006575	modified amino acid metabolic process	122	178	7.064e-04
GO:BP	GO:2001032	regulation of double-strand break repair via nonhomologous end joining	25	28	7.263e-04
GO:BP	GO:0150052	regulation of postsynapse assembly	37	45	7.295e-04
GO:BP	GO:0048640	negative regulation of developmental growth	70	95	7.298e-04
GO:BP	GO:0006098	pentose-phosphate shunt	19	20	7.487e-04
GO:BP	GO:0006684	sphingomyelin metabolic process	19	20	7.487e-04
GO:BP	GO:0071498	cellular response to fluid shear stress	19	20	7.487e-04
GO:BP	GO:1901201	regulation of extracellular matrix assembly	19	20	7.487e-04
GO:BP	GO:0046782	regulation of viral transcription	19	20	7.487e-04
GO:BP	GO:0036499	PERK-mediated unfolded protein response	19	20	7.487e-04
GO:BP	GO:0061003	positive regulation of dendritic spine morphogenesis	19	20	7.487e-04
GO:BP	GO:0002097	tRNA wobble base modification	19	20	7.487e-04
GO:BP	GO:0030150	protein import into mitochondrial matrix	19	20	7.487e-04
GO:BP	GO:2000786	positive regulation of autophagosome assembly	19	20	7.487e-04
GO:BP	GO:0043276	anoikis	30	35	7.552e-04
GO:BP	GO:0031114	regulation of microtubule depolymerization	30	35	7.552e-04
GO:BP	GO:0031952	regulation of protein autophosphorylation	30	35	7.552e-04
GO:BP	GO:0000819	sister chromatid segregation	156	234	7.585e-04
GO:BP	GO:1905314	semi-lunar valve development	39	48	7.759e-04
GO:BP	GO:0097106	postsynaptic density organization	39	48	7.759e-04
GO:BP	GO:0034331	cell junction maintenance	39	48	7.759e-04
GO:BP	GO:0002090	regulation of receptor internalization	55	72	7.896e-04
GO:BP	GO:0000027	ribosomal large subunit assembly	22	24	7.896e-04
GO:BP	GO:0043153	entrainment of circadian clock by photoperiod	22	24	7.896e-04
GO:BP	GO:0071479	cellular response to ionizing radiation	55	72	7.896e-04
GO:BP	GO:0051131	chaperone-mediated protein complex assembly	22	24	7.896e-04
GO:BP	GO:0006488	dolichol-linked oligosaccharide biosynthetic process	22	24	7.896e-04
GO:BP	GO:0006809	nitric oxide biosynthetic process	55	72	7.896e-04
GO:BP	GO:0050708	regulation of protein secretion	177	269	7.945e-04
GO:BP	GO:1902743	regulation of lamellipodium organization	41	51	8.105e-04
GO:BP	GO:0048009	insulin-like growth factor receptor signaling pathway	41	51	8.105e-04
GO:BP	GO:0048255	mRNA stabilization	53	69	8.113e-04
GO:BP	GO:0051123	RNA polymerase II preinitiation complex assembly	53	69	8.113e-04
GO:BP	GO:0007528	neuromuscular junction development	43	54	8.326e-04
GO:BP	GO:0046605	regulation of centrosome cycle	43	54	8.326e-04
GO:BP	GO:0006110	regulation of glycolytic process	43	54	8.326e-04
GO:BP	GO:0033121	regulation of purine nucleotide catabolic process	43	54	8.326e-04
GO:BP	GO:0030811	regulation of nucleotide catabolic process	43	54	8.326e-04
GO:BP	GO:0061245	establishment or maintenance of bipolar cell polarity	45	57	8.445e-04
GO:BP	GO:0001738	morphogenesis of a polarized epithelium	45	57	8.445e-04
GO:BP	GO:0035088	establishment or maintenance of apical/basal cell polarity	45	57	8.445e-04
GO:BP	GO:0000041	transition metal ion transport	73	100	8.461e-04
GO:BP	GO:0051347	positive regulation of transferase activity	193	296	8.599e-04
GO:BP	GO:0046831	regulation of RNA export from nucleus	15	15	8.600e-04
GO:BP	GO:0006999	nuclear pore organization	15	15	8.600e-04
GO:BP	GO:0071027	nuclear RNA surveillance	15	15	8.600e-04
GO:BP	GO:0033750	ribosome localization	15	15	8.600e-04
GO:BP	GO:0060211	regulation of nuclear-transcribed mRNA poly(A) tail shortening	15	15	8.600e-04
GO:BP	GO:1901836	regulation of transcription of nucleolar large rRNA by RNA polymerase I	15	15	8.600e-04
GO:BP	GO:0061307	cardiac neural crest cell differentiation involved in heart development	15	15	8.600e-04
GO:BP	GO:1904507	positive regulation of telomere maintenance in response to DNA damage	15	15	8.600e-04
GO:BP	GO:0061308	cardiac neural crest cell development involved in heart development	15	15	8.600e-04
GO:BP	GO:1905666	regulation of protein localization to endosome	15	15	8.600e-04
GO:BP	GO:0034616	response to laminar fluid shear stress	15	15	8.600e-04
GO:BP	GO:0000054	ribosomal subunit export from nucleus	15	15	8.600e-04
GO:BP	GO:0060413	atrial septum morphogenesis	15	15	8.600e-04
GO:BP	GO:0048659	smooth muscle cell proliferation	100	143	8.707e-04
GO:BP	GO:0045023	G0 to G1 transition	32	38	8.720e-04
GO:BP	GO:0006516	glycoprotein catabolic process	32	38	8.720e-04
GO:BP	GO:1902110	positive regulation of mitochondrial membrane permeability involved in apoptotic process	32	38	8.720e-04
GO:BP	GO:0035383	thioester metabolic process	71	97	8.989e-04
GO:BP	GO:0046330	positive regulation of JNK cascade	71	97	8.989e-04
GO:BP	GO:0006637	acyl-CoA metabolic process	71	97	8.989e-04
GO:BP	GO:0046928	regulation of neurotransmitter secretion	62	83	9.028e-04
GO:BP	GO:0030947	regulation of vascular endothelial growth factor receptor signaling pathway	27	31	9.430e-04
GO:BP	GO:0051491	positive regulation of filopodium assembly	27	31	9.430e-04
GO:BP	GO:0033500	carbohydrate homeostasis	173	263	9.480e-04
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	88	124	9.543e-04
GO:BP	GO:0021954	central nervous system neuron development	69	94	9.608e-04
GO:BP	GO:0030641	regulation of cellular pH	69	94	9.608e-04
GO:BP	GO:0071248	cellular response to metal ion	130	192	9.628e-04
GO:BP	GO:0044319	wound healing, spreading of cells	34	41	9.771e-04
GO:BP	GO:1902305	regulation of sodium ion transmembrane transport	34	41	9.771e-04
GO:BP	GO:0045454	cell redox homeostasis	34	41	9.771e-04
GO:BP	GO:0090505	epiboly involved in wound healing	34	41	9.771e-04
GO:BP	GO:0032411	positive regulation of transporter activity	58	77	9.960e-04
GO:BP	GO:0009743	response to carbohydrate	162	245	1.029e-03
GO:BP	GO:0050680	negative regulation of epithelial cell proliferation	96	137	1.036e-03
GO:BP	GO:0072164	mesonephric tubule development	74	102	1.039e-03
GO:BP	GO:0072163	mesonephric epithelium development	74	102	1.039e-03
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	56	74	1.040e-03
GO:BP	GO:0045834	positive regulation of lipid metabolic process	91	129	1.041e-03
GO:BP	GO:0045646	regulation of erythrocyte differentiation	36	44	1.062e-03
GO:BP	GO:0070373	negative regulation of ERK1 and ERK2 cascade	52	68	1.122e-03
GO:BP	GO:1901607	alpha-amino acid biosynthetic process	52	68	1.122e-03
GO:BP	GO:0010634	positive regulation of epithelial cell migration	38	47	1.125e-03
GO:BP	GO:0010824	regulation of centrosome duplication	38	47	1.125e-03
GO:BP	GO:0140014	mitotic nuclear division	184	282	1.132e-03
GO:BP	GO:0016233	telomere capping	24	27	1.138e-03
GO:BP	GO:0048011	neurotrophin TRK receptor signaling pathway	24	27	1.138e-03
GO:BP	GO:0060544	regulation of necroptotic process	24	27	1.138e-03
GO:BP	GO:0043507	positive regulation of JUN kinase activity	24	27	1.138e-03
GO:BP	GO:0010721	negative regulation of cell development	175	267	1.139e-03
GO:BP	GO:0042593	glucose homeostasis	172	262	1.139e-03
GO:BP	GO:0006654	phosphatidic acid biosynthetic process	29	34	1.144e-03
GO:BP	GO:0043516	regulation of DNA damage response, signal transduction by p53 class mediator	29	34	1.144e-03
GO:BP	GO:0018198	peptidyl-cysteine modification	29	34	1.144e-03
GO:BP	GO:0051647	nucleus localization	29	34	1.144e-03
GO:BP	GO:1902235	regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	29	34	1.144e-03
GO:BP	GO:0033013	tetrapyrrole metabolic process	50	65	1.147e-03
GO:BP	GO:0031103	axon regeneration	40	50	1.160e-03
GO:BP	GO:0060976	coronary vasculature development	40	50	1.160e-03
GO:BP	GO:1900024	regulation of substrate adhesion-dependent cell spreading	48	62	1.171e-03
GO:BP	GO:0051148	negative regulation of muscle cell differentiation	48	62	1.171e-03
GO:BP	GO:0032648	regulation of interferon-beta production	46	59	1.186e-03
GO:BP	GO:0032608	interferon-beta production	46	59	1.186e-03
GO:BP	GO:0086002	cardiac muscle cell action potential involved in contraction	46	59	1.186e-03
GO:BP	GO:0031529	ruffle organization	44	56	1.190e-03
GO:BP	GO:0010718	positive regulation of epithelial to mesenchymal transition	44	56	1.190e-03
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	97	139	1.205e-03
GO:BP	GO:0045860	positive regulation of protein kinase activity	158	239	1.233e-03
GO:BP	GO:0099514	synaptic vesicle cytoskeletal transport	18	19	1.233e-03
GO:BP	GO:1902992	negative regulation of amyloid precursor protein catabolic process	18	19	1.233e-03
GO:BP	GO:0099517	synaptic vesicle transport along microtubule	18	19	1.233e-03
GO:BP	GO:0018022	peptidyl-lysine methylation	18	19	1.233e-03
GO:BP	GO:0046931	pore complex assembly	18	19	1.233e-03
GO:BP	GO:0097284	hepatocyte apoptotic process	18	19	1.233e-03
GO:BP	GO:0035269	protein O-linked mannosylation	18	19	1.233e-03
GO:BP	GO:0035720	intraciliary anterograde transport	18	19	1.233e-03
GO:BP	GO:0110154	RNA decapping	18	19	1.233e-03
GO:BP	GO:0048490	anterograde synaptic vesicle transport	18	19	1.233e-03
GO:BP	GO:1903232	melanosome assembly	18	19	1.233e-03
GO:BP	GO:1902774	late endosome to lysosome transport	21	23	1.263e-03
GO:BP	GO:0003283	atrial septum development	21	23	1.263e-03
GO:BP	GO:0039702	viral budding via host ESCRT complex	21	23	1.263e-03
GO:BP	GO:0035331	negative regulation of hippo signaling	21	23	1.263e-03
GO:BP	GO:0006851	mitochondrial calcium ion transmembrane transport	21	23	1.263e-03
GO:BP	GO:1901983	regulation of protein acetylation	21	23	1.263e-03
GO:BP	GO:0030901	midbrain development	68	93	1.267e-03
GO:BP	GO:0033209	tumor necrosis factor-mediated signaling pathway	80	112	1.305e-03
GO:BP	GO:0003230	cardiac atrium development	31	37	1.307e-03
GO:BP	GO:0051592	response to calcium ion	95	136	1.308e-03
GO:BP	GO:0051453	regulation of intracellular pH	66	90	1.358e-03
GO:BP	GO:0001657	ureteric bud development	73	101	1.358e-03
GO:BP	GO:0048844	artery morphogenesis	55	73	1.417e-03
GO:BP	GO:0003143	embryonic heart tube morphogenesis	55	73	1.417e-03
GO:BP	GO:0086091	regulation of heart rate by cardiac conduction	33	40	1.450e-03
GO:BP	GO:0060391	positive regulation of SMAD protein signal transduction	33	40	1.450e-03
GO:BP	GO:1904738	vascular associated smooth muscle cell migration	26	30	1.456e-03
GO:BP	GO:1904357	negative regulation of telomere maintenance via telomere lengthening	26	30	1.456e-03
GO:BP	GO:0000002	mitochondrial genome maintenance	26	30	1.456e-03
GO:BP	GO:0001778	plasma membrane repair	26	30	1.456e-03
GO:BP	GO:0032367	intracellular cholesterol transport	26	30	1.456e-03
GO:BP	GO:0032414	positive regulation of ion transmembrane transporter activity	53	70	1.478e-03
GO:BP	GO:0046847	filopodium assembly	53	70	1.478e-03
GO:BP	GO:0060972	left/right pattern formation	101	146	1.481e-03
GO:BP	GO:1904353	regulation of telomere capping	14	14	1.491e-03
GO:BP	GO:0098734	macromolecule depalmitoylation	14	14	1.491e-03
GO:BP	GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation	14	14	1.491e-03
GO:BP	GO:0007008	outer mitochondrial membrane organization	14	14	1.491e-03
GO:BP	GO:1901985	positive regulation of protein acetylation	14	14	1.491e-03
GO:BP	GO:1901203	positive regulation of extracellular matrix assembly	14	14	1.491e-03
GO:BP	GO:0035970	peptidyl-threonine dephosphorylation	14	14	1.491e-03
GO:BP	GO:0051645	Golgi localization	14	14	1.491e-03
GO:BP	GO:0072393	microtubule anchoring at microtubule organizing center	14	14	1.491e-03
GO:BP	GO:0045040	protein insertion into mitochondrial outer membrane	14	14	1.491e-03
GO:BP	GO:0035721	intraciliary retrograde transport	14	14	1.491e-03
GO:BP	GO:1905668	positive regulation of protein localization to endosome	14	14	1.491e-03
GO:BP	GO:1904350	regulation of protein catabolic process in the vacuole	14	14	1.491e-03
GO:BP	GO:0032933	SREBP signaling pathway	14	14	1.491e-03
GO:BP	GO:0035791	platelet-derived growth factor receptor-beta signaling pathway	14	14	1.491e-03
GO:BP	GO:0001885	endothelial cell development	51	67	1.527e-03
GO:BP	GO:0016042	lipid catabolic process	226	354	1.537e-03
GO:BP	GO:1990000	amyloid fibril formation	35	43	1.538e-03
GO:BP	GO:0030149	sphingolipid catabolic process	35	43	1.538e-03
GO:BP	GO:0009066	aspartate family amino acid metabolic process	35	43	1.538e-03
GO:BP	GO:0099563	modification of synaptic structure	35	43	1.538e-03
GO:BP	GO:0030902	hindbrain development	112	164	1.540e-03
GO:BP	GO:0000281	mitotic cytokinesis	69	95	1.559e-03
GO:BP	GO:0048524	positive regulation of viral process	49	64	1.576e-03
GO:BP	GO:0030042	actin filament depolymerization	45	58	1.656e-03
GO:BP	GO:0030837	negative regulation of actin filament polymerization	45	58	1.656e-03
GO:BP	GO:0042181	ketone biosynthetic process	39	49	1.656e-03
GO:BP	GO:0140374	antiviral innate immune response	43	55	1.674e-03
GO:BP	GO:0030838	positive regulation of actin filament polymerization	41	52	1.675e-03
GO:BP	GO:0009890	negative regulation of biosynthetic process	1620	2813	1.681e-03
GO:BP	GO:0010565	regulation of ketone metabolic process	89	127	1.690e-03
GO:BP	GO:0051607	defense response to virus	205	319	1.721e-03
GO:BP	GO:0021591	ventricular system development	28	33	1.726e-03
GO:BP	GO:0060421	positive regulation of heart growth	28	33	1.726e-03
GO:BP	GO:0031116	positive regulation of microtubule polymerization	28	33	1.726e-03
GO:BP	GO:0060325	face morphogenesis	28	33	1.726e-03
GO:BP	GO:0060993	kidney morphogenesis	72	100	1.774e-03
GO:BP	GO:0006493	protein O-linked glycosylation	72	100	1.774e-03
GO:BP	GO:0003181	atrioventricular valve morphogenesis	23	26	1.775e-03
GO:BP	GO:0061744	motor behavior	23	26	1.775e-03
GO:BP	GO:0005980	glycogen catabolic process	23	26	1.775e-03
GO:BP	GO:1905207	regulation of cardiocyte differentiation	23	26	1.775e-03
GO:BP	GO:0007039	protein catabolic process in the vacuole	23	26	1.775e-03
GO:BP	GO:0046323	D-glucose import	56	75	1.821e-03
GO:BP	GO:0007229	integrin-mediated signaling pathway	82	116	1.850e-03
GO:BP	GO:0051260	protein homooligomerization	136	204	1.872e-03
GO:BP	GO:0048661	positive regulation of smooth muscle cell proliferation	63	86	1.926e-03
GO:BP	GO:0099010	modification of postsynaptic structure	30	36	1.954e-03
GO:BP	GO:0006301	postreplication repair	30	36	1.954e-03
GO:BP	GO:0035459	vesicle cargo loading	30	36	1.954e-03
GO:BP	GO:0006904	vesicle docking involved in exocytosis	30	36	1.954e-03
GO:BP	GO:0070306	lens fiber cell differentiation	30	36	1.954e-03
GO:BP	GO:0090630	activation of GTPase activity	30	36	1.954e-03
GO:BP	GO:0032885	regulation of polysaccharide biosynthetic process	30	36	1.954e-03
GO:BP	GO:0051150	regulation of smooth muscle cell differentiation	30	36	1.954e-03
GO:BP	GO:0030199	collagen fibril organization	52	69	2.014e-03
GO:BP	GO:0006879	intracellular iron ion homeostasis	52	69	2.014e-03
GO:BP	GO:0090050	positive regulation of cell migration involved in sprouting angiogenesis	20	22	2.036e-03
GO:BP	GO:0031954	positive regulation of protein autophosphorylation	20	22	2.036e-03
GO:BP	GO:1900407	regulation of cellular response to oxidative stress	20	22	2.036e-03
GO:BP	GO:0032042	mitochondrial DNA metabolic process	20	22	2.036e-03
GO:BP	GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process	20	22	2.036e-03
GO:BP	GO:1900242	regulation of synaptic vesicle endocytosis	20	22	2.036e-03
GO:BP	GO:0032785	negative regulation of DNA-templated transcription, elongation	20	22	2.036e-03
GO:BP	GO:1905146	lysosomal protein catabolic process	20	22	2.036e-03
GO:BP	GO:0008090	retrograde axonal transport	20	22	2.036e-03
GO:BP	GO:0043555	regulation of translation in response to stress	20	22	2.036e-03
GO:BP	GO:0086026	atrial cardiac muscle cell to AV node cell signaling	17	18	2.037e-03
GO:BP	GO:0086014	atrial cardiac muscle cell action potential	17	18	2.037e-03
GO:BP	GO:0090110	COPII-coated vesicle cargo loading	17	18	2.037e-03
GO:BP	GO:0072673	lamellipodium morphogenesis	17	18	2.037e-03
GO:BP	GO:0086066	atrial cardiac muscle cell to AV node cell communication	17	18	2.037e-03
GO:BP	GO:0043923	positive regulation by host of viral transcription	17	18	2.037e-03
GO:BP	GO:0061333	renal tubule morphogenesis	61	83	2.037e-03
GO:BP	GO:0062099	negative regulation of programmed necrotic cell death	17	18	2.037e-03
GO:BP	GO:0019896	axonal transport of mitochondrion	17	18	2.037e-03
GO:BP	GO:1902430	negative regulation of amyloid-beta formation	17	18	2.037e-03
GO:BP	GO:0061323	cell proliferation involved in heart morphogenesis	17	18	2.037e-03
GO:BP	GO:2000136	regulation of cell proliferation involved in heart morphogenesis	17	18	2.037e-03
GO:BP	GO:0045722	positive regulation of gluconeogenesis	17	18	2.037e-03
GO:BP	GO:0015936	coenzyme A metabolic process	17	18	2.037e-03
GO:BP	GO:0016125	sterol metabolic process	109	160	2.090e-03
GO:BP	GO:0051125	regulation of actin nucleation	32	39	2.112e-03
GO:BP	GO:0120033	negative regulation of plasma membrane bounded cell projection assembly	32	39	2.112e-03
GO:BP	GO:0072593	reactive oxygen species metabolic process	152	231	2.119e-03
GO:BP	GO:0031347	regulation of defense response	489	809	2.119e-03
GO:BP	GO:0046394	carboxylic acid biosynthetic process	205	320	2.157e-03
GO:BP	GO:1990874	vascular associated smooth muscle cell proliferation	48	63	2.164e-03
GO:BP	GO:0010803	regulation of tumor necrosis factor-mediated signaling pathway	48	63	2.164e-03
GO:BP	GO:0006518	peptide metabolic process	48	63	2.164e-03
GO:BP	GO:0048660	regulation of smooth muscle cell proliferation	96	139	2.201e-03
GO:BP	GO:0051053	negative regulation of DNA metabolic process	96	139	2.201e-03
GO:BP	GO:0051156	glucose 6-phosphate metabolic process	25	29	2.218e-03
GO:BP	GO:0003171	atrioventricular valve development	25	29	2.218e-03
GO:BP	GO:0048679	regulation of axon regeneration	25	29	2.218e-03
GO:BP	GO:1903034	regulation of response to wounding	115	170	2.219e-03
GO:BP	GO:0019432	triglyceride biosynthetic process	34	42	2.230e-03
GO:BP	GO:0043124	negative regulation of canonical NF-kappaB signal transduction	46	60	2.231e-03
GO:BP	GO:0080164	regulation of nitric oxide metabolic process	46	60	2.231e-03
GO:BP	GO:0099172	presynapse organization	46	60	2.231e-03
GO:BP	GO:0009749	response to glucose	138	208	2.275e-03
GO:BP	GO:0001755	neural crest cell migration	44	57	2.288e-03
GO:BP	GO:0030865	cortical cytoskeleton organization	44	57	2.288e-03
GO:BP	GO:0051452	intracellular pH reduction	44	57	2.288e-03
GO:BP	GO:1902895	positive regulation of miRNA transcription	44	57	2.288e-03
GO:BP	GO:0009746	response to hexose	141	213	2.288e-03
GO:BP	GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	71	99	2.289e-03
GO:BP	GO:0008652	amino acid biosynthetic process	57	77	2.293e-03
GO:BP	GO:0045663	positive regulation of myoblast differentiation	36	45	2.301e-03
GO:BP	GO:0021695	cerebellar cortex development	42	54	2.327e-03
GO:BP	GO:0055021	regulation of cardiac muscle tissue growth	42	54	2.327e-03
GO:BP	GO:0046466	membrane lipid catabolic process	38	48	2.339e-03
GO:BP	GO:0120163	negative regulation of cold-induced thermogenesis	38	48	2.339e-03
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	40	51	2.342e-03
GO:BP	GO:0046463	acylglycerol biosynthetic process	40	51	2.342e-03
GO:BP	GO:0046460	neutral lipid biosynthetic process	40	51	2.342e-03
GO:BP	GO:0046578	regulation of Ras protein signal transduction	40	51	2.342e-03
GO:BP	GO:0055088	lipid homeostasis	113	167	2.425e-03
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	116	172	2.492e-03
GO:BP	GO:2001257	regulation of cation channel activity	62	85	2.523e-03
GO:BP	GO:0034284	response to monosaccharide	145	220	2.533e-03
GO:BP	GO:0060348	bone development	145	220	2.533e-03
GO:BP	GO:1901655	cellular response to ketone	79	112	2.557e-03
GO:BP	GO:1902253	regulation of intrinsic apoptotic signaling pathway by p53 class mediator	27	32	2.559e-03
GO:BP	GO:0097707	ferroptosis	13	13	2.559e-03
GO:BP	GO:0035542	regulation of SNARE complex assembly	13	13	2.559e-03
GO:BP	GO:0001682	tRNA 5’-leader removal	13	13	2.559e-03
GO:BP	GO:0090646	mitochondrial tRNA processing	13	13	2.559e-03
GO:BP	GO:1904380	endoplasmic reticulum mannose trimming	13	13	2.559e-03
GO:BP	GO:0006465	signal peptide processing	13	13	2.559e-03
GO:BP	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	13	13	2.559e-03
GO:BP	GO:0042558	pteridine-containing compound metabolic process	27	32	2.559e-03
GO:BP	GO:0090158	endoplasmic reticulum membrane organization	13	13	2.559e-03
GO:BP	GO:0003174	mitral valve development	13	13	2.559e-03
GO:BP	GO:0031958	nuclear receptor-mediated corticosteroid signaling pathway	13	13	2.559e-03
GO:BP	GO:0061795	Golgi lumen acidification	13	13	2.559e-03
GO:BP	GO:1904152	regulation of retrograde protein transport, ER to cytosol	13	13	2.559e-03
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	53	71	2.559e-03
GO:BP	GO:0033235	positive regulation of protein sumoylation	13	13	2.559e-03
GO:BP	GO:0043558	regulation of translational initiation in response to stress	13	13	2.559e-03
GO:BP	GO:0034333	adherens junction assembly	13	13	2.559e-03
GO:BP	GO:0009304	tRNA transcription	13	13	2.559e-03
GO:BP	GO:0090317	negative regulation of intracellular protein transport	27	32	2.559e-03
GO:BP	GO:0034551	mitochondrial respiratory chain complex III assembly	13	13	2.559e-03
GO:BP	GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	13	13	2.559e-03
GO:BP	GO:0010867	positive regulation of triglyceride biosynthetic process	13	13	2.559e-03
GO:BP	GO:0045039	protein insertion into mitochondrial inner membrane	13	13	2.559e-03
GO:BP	GO:0017062	respiratory chain complex III assembly	13	13	2.559e-03
GO:BP	GO:0060966	regulation of gene silencing by regulatory ncRNA	27	32	2.559e-03
GO:BP	GO:0060674	placenta blood vessel development	27	32	2.559e-03
GO:BP	GO:0006865	amino acid transport	111	164	2.636e-03
GO:BP	GO:0032103	positive regulation of response to external stimulus	392	642	2.694e-03
GO:BP	GO:1903779	regulation of cardiac conduction	22	25	2.739e-03
GO:BP	GO:0007097	nuclear migration	22	25	2.739e-03
GO:BP	GO:1901659	glycosyl compound biosynthetic process	22	25	2.739e-03
GO:BP	GO:0070861	regulation of protein exit from endoplasmic reticulum	22	25	2.739e-03
GO:BP	GO:0070841	inclusion body assembly	22	25	2.739e-03
GO:BP	GO:0032400	melanosome localization	22	25	2.739e-03
GO:BP	GO:0019751	polyol metabolic process	77	109	2.750e-03
GO:BP	GO:0048144	fibroblast proliferation	77	109	2.750e-03
GO:BP	GO:0009612	response to mechanical stimulus	146	222	2.751e-03
GO:BP	GO:0051145	smooth muscle cell differentiation	49	65	2.814e-03
GO:BP	GO:2000630	positive regulation of miRNA metabolic process	49	65	2.814e-03
GO:BP	GO:0048145	regulation of fibroblast proliferation	65	90	2.852e-03
GO:BP	GO:0090162	establishment of epithelial cell polarity	29	35	2.853e-03
GO:BP	GO:0014808	release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	29	35	2.853e-03
GO:BP	GO:0071482	cellular response to light stimulus	85	122	2.928e-03
GO:BP	GO:0033619	membrane protein proteolysis	47	62	2.944e-03
GO:BP	GO:0051851	host-mediated perturbation of symbiont process	75	106	2.995e-03
GO:BP	GO:0001823	mesonephros development	75	106	2.995e-03
GO:BP	GO:0061326	renal tubule development	75	106	2.995e-03
GO:BP	GO:0090497	mesenchymal cell migration	45	59	3.063e-03
GO:BP	GO:0098698	postsynaptic specialization assembly	31	38	3.069e-03
GO:BP	GO:0045773	positive regulation of axon extension	31	38	3.069e-03
GO:BP	GO:0031112	positive regulation of microtubule polymerization or depolymerization	31	38	3.069e-03
GO:BP	GO:0039532	negative regulation of cytoplasmic pattern recognition receptor signaling pathway	43	56	3.164e-03
GO:BP	GO:0170038	proteinogenic amino acid biosynthetic process	43	56	3.164e-03
GO:BP	GO:0050792	regulation of viral process	107	158	3.176e-03
GO:BP	GO:0001935	endothelial cell proliferation	107	158	3.176e-03
GO:BP	GO:1901532	regulation of hematopoietic progenitor cell differentiation	33	41	3.213e-03
GO:BP	GO:0072663	establishment of protein localization to peroxisome	19	21	3.223e-03
GO:BP	GO:0010288	response to lead ion	19	21	3.223e-03
GO:BP	GO:1902018	negative regulation of cilium assembly	19	21	3.223e-03
GO:BP	GO:0072662	protein localization to peroxisome	19	21	3.223e-03
GO:BP	GO:0045912	negative regulation of carbohydrate metabolic process	41	53	3.238e-03
GO:BP	GO:0030201	heparan sulfate proteoglycan metabolic process	35	44	3.282e-03
GO:BP	GO:0060338	regulation of type I interferon-mediated signaling pathway	35	44	3.282e-03
GO:BP	GO:0097178	ruffle assembly	35	44	3.282e-03
GO:BP	GO:0003176	aortic valve development	35	44	3.282e-03
GO:BP	GO:0032506	cytokinetic process	39	50	3.286e-03
GO:BP	GO:0060038	cardiac muscle cell proliferation	39	50	3.286e-03
GO:BP	GO:0034766	negative regulation of monoatomic ion transmembrane transport	61	84	3.299e-03
GO:BP	GO:0010463	mesenchymal cell proliferation	37	47	3.301e-03
GO:BP	GO:0030073	insulin secretion	139	211	3.301e-03
GO:BP	GO:0006103	2-oxoglutarate metabolic process	16	17	3.335e-03
GO:BP	GO:2000369	regulation of clathrin-dependent endocytosis	16	17	3.335e-03
GO:BP	GO:0141198	protein branched polyubiquitination	16	17	3.335e-03
GO:BP	GO:0002098	tRNA wobble uridine modification	16	17	3.335e-03
GO:BP	GO:0070131	positive regulation of mitochondrial translation	16	17	3.335e-03
GO:BP	GO:0007000	nucleolus organization	16	17	3.335e-03
GO:BP	GO:0006991	response to sterol depletion	16	17	3.335e-03
GO:BP	GO:0034349	glial cell apoptotic process	16	17	3.335e-03
GO:BP	GO:0044790	suppression of viral release by host	16	17	3.335e-03
GO:BP	GO:0071243	cellular response to arsenic-containing substance	16	17	3.335e-03
GO:BP	GO:0003209	cardiac atrium morphogenesis	24	28	3.342e-03
GO:BP	GO:0032801	receptor catabolic process	24	28	3.342e-03
GO:BP	GO:0032469	endoplasmic reticulum calcium ion homeostasis	24	28	3.342e-03
GO:BP	GO:1901021	positive regulation of calcium ion transmembrane transporter activity	24	28	3.342e-03
GO:BP	GO:1904752	regulation of vascular associated smooth muscle cell migration	24	28	3.342e-03
GO:BP	GO:0099558	maintenance of synapse structure	24	28	3.342e-03
GO:BP	GO:0010592	positive regulation of lamellipodium assembly	24	28	3.342e-03
GO:BP	GO:0046513	ceramide biosynthetic process	52	70	3.414e-03
GO:BP	GO:0048645	animal organ formation	52	70	3.414e-03
GO:BP	GO:0032088	negative regulation of NF-kappaB transcription factor activity	52	70	3.414e-03
GO:BP	GO:0046889	positive regulation of lipid biosynthetic process	66	92	3.431e-03
GO:BP	GO:0035023	regulation of Rho protein signal transduction	64	89	3.731e-03
GO:BP	GO:0050905	neuromuscular process	117	175	3.782e-03
GO:BP	GO:0043271	negative regulation of monoatomic ion transport	79	113	3.798e-03
GO:BP	GO:0021766	hippocampus development	69	97	3.829e-03
GO:BP	GO:1903706	regulation of hemopoiesis	265	425	3.841e-03
GO:BP	GO:0006885	regulation of pH	74	105	3.841e-03
GO:BP	GO:0090288	negative regulation of cellular response to growth factor stimulus	74	105	3.841e-03
GO:BP	GO:0060147	regulation of post-transcriptional gene silencing	26	31	3.859e-03
GO:BP	GO:0045724	positive regulation of cilium assembly	26	31	3.859e-03
GO:BP	GO:0051701	biological process involved in interaction with host	123	185	3.871e-03
GO:BP	GO:0007368	determination of left/right symmetry	95	139	3.899e-03
GO:BP	GO:0034502	protein localization to chromosome	87	126	3.906e-03
GO:BP	GO:0043410	positive regulation of MAPK cascade	283	456	3.906e-03
GO:BP	GO:0009755	hormone-mediated signaling pathway	147	225	3.946e-03
GO:BP	GO:1904705	regulation of vascular associated smooth muscle cell proliferation	46	61	4.022e-03
GO:BP	GO:0008284	positive regulation of cell population proliferation	569	954	4.036e-03
GO:BP	GO:0032481	positive regulation of type I interferon production	55	75	4.059e-03
GO:BP	GO:0010827	regulation of D-glucose transmembrane transport	55	75	4.059e-03
GO:BP	GO:0015748	organophosphate ester transport	115	172	4.149e-03
GO:BP	GO:0060021	roof of mouth development	67	94	4.150e-03
GO:BP	GO:0016053	organic acid biosynthetic process	205	323	4.166e-03
GO:BP	GO:0048534	hematopoietic or lymphoid organ development	72	102	4.181e-03
GO:BP	GO:0045428	regulation of nitric oxide biosynthetic process	44	58	4.203e-03
GO:BP	GO:0120009	intermembrane lipid transfer	28	34	4.222e-03
GO:BP	GO:0086005	ventricular cardiac muscle cell action potential	28	34	4.222e-03
GO:BP	GO:0030517	negative regulation of axon extension	28	34	4.222e-03
GO:BP	GO:0097345	mitochondrial outer membrane permeabilization	28	34	4.222e-03
GO:BP	GO:0060603	mammary gland duct morphogenesis	28	34	4.222e-03
GO:BP	GO:1901673	regulation of mitotic spindle assembly	21	24	4.261e-03
GO:BP	GO:0036119	response to platelet-derived growth factor	21	24	4.261e-03
GO:BP	GO:0051560	mitochondrial calcium ion homeostasis	21	24	4.261e-03
GO:BP	GO:1902993	positive regulation of amyloid precursor protein catabolic process	21	24	4.261e-03
GO:BP	GO:0046835	carbohydrate phosphorylation	21	24	4.261e-03
GO:BP	GO:0014912	negative regulation of smooth muscle cell migration	21	24	4.261e-03
GO:BP	GO:0033233	regulation of protein sumoylation	21	24	4.261e-03
GO:BP	GO:0042659	regulation of cell fate specification	21	24	4.261e-03
GO:BP	GO:0003148	outflow tract septum morphogenesis	21	24	4.261e-03
GO:BP	GO:0007626	locomotory behavior	145	222	4.309e-03
GO:BP	GO:0051101	regulation of DNA binding	53	72	4.316e-03
GO:BP	GO:0072028	nephron morphogenesis	60	83	4.320e-03
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	42	55	4.342e-03
GO:BP	GO:0048286	lung alveolus development	42	55	4.342e-03
GO:BP	GO:0033540	fatty acid beta-oxidation using acyl-CoA oxidase	12	12	4.400e-03
GO:BP	GO:0140627	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway	12	12	4.400e-03
GO:BP	GO:0031126	sno(s)RNA 3’-end processing	12	12	4.400e-03
GO:BP	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	12	12	4.400e-03
GO:BP	GO:0061723	glycophagy	12	12	4.400e-03
GO:BP	GO:0110075	regulation of ferroptosis	12	12	4.400e-03
GO:BP	GO:0006448	regulation of translational elongation	12	12	4.400e-03
GO:BP	GO:1904872	regulation of telomerase RNA localization to Cajal body	12	12	4.400e-03
GO:BP	GO:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	12	12	4.400e-03
GO:BP	GO:1905165	regulation of lysosomal protein catabolic process	12	12	4.400e-03
GO:BP	GO:1902946	protein localization to early endosome	12	12	4.400e-03
GO:BP	GO:1900370	positive regulation of post-transcriptional gene silencing by RNA	12	12	4.400e-03
GO:BP	GO:1990253	cellular response to leucine starvation	12	12	4.400e-03
GO:BP	GO:0042797	tRNA transcription by RNA polymerase III	12	12	4.400e-03
GO:BP	GO:0050847	progesterone receptor signaling pathway	12	12	4.400e-03
GO:BP	GO:0097576	vacuole fusion	12	12	4.400e-03
GO:BP	GO:0042921	nuclear receptor-mediated glucocorticoid signaling pathway	12	12	4.400e-03
GO:BP	GO:0061309	cardiac neural crest cell development involved in outflow tract morphogenesis	12	12	4.400e-03
GO:BP	GO:2000637	positive regulation of miRNA-mediated gene silencing	12	12	4.400e-03
GO:BP	GO:0000491	small nucleolar ribonucleoprotein complex assembly	12	12	4.400e-03
GO:BP	GO:0034454	microtubule anchoring at centrosome	12	12	4.400e-03
GO:BP	GO:1904779	regulation of protein localization to centrosome	12	12	4.400e-03
GO:BP	GO:0038026	reelin-mediated signaling pathway	12	12	4.400e-03
GO:BP	GO:0098911	regulation of ventricular cardiac muscle cell action potential	12	12	4.400e-03
GO:BP	GO:1901844	regulation of cell communication by electrical coupling involved in cardiac conduction	12	12	4.400e-03
GO:BP	GO:0060148	positive regulation of post-transcriptional gene silencing	12	12	4.400e-03
GO:BP	GO:0003183	mitral valve morphogenesis	12	12	4.400e-03
GO:BP	GO:1903514	release of sequestered calcium ion into cytosol by endoplasmic reticulum	30	37	4.407e-03
GO:BP	GO:0042157	lipoprotein metabolic process	65	91	4.424e-03
GO:BP	GO:0003197	endocardial cushion development	40	52	4.430e-03
GO:BP	GO:0010332	response to gamma radiation	40	52	4.430e-03
GO:BP	GO:0030510	regulation of BMP signaling pathway	75	107	4.438e-03
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	113	169	4.471e-03
GO:BP	GO:0071616	acyl-CoA biosynthetic process	38	49	4.533e-03
GO:BP	GO:0035384	thioester biosynthetic process	38	49	4.533e-03
GO:BP	GO:0061082	myeloid leukocyte cytokine production	38	49	4.533e-03
GO:BP	GO:0033120	positive regulation of RNA splicing	38	49	4.533e-03
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	51	69	4.536e-03
GO:BP	GO:0070266	necroptotic process	32	40	4.540e-03
GO:BP	GO:0010719	negative regulation of epithelial to mesenchymal transition	32	40	4.540e-03
GO:BP	GO:0042886	amide transport	210	332	4.550e-03
GO:BP	GO:0045913	positive regulation of carbohydrate metabolic process	58	80	4.583e-03
GO:BP	GO:0006275	regulation of DNA replication	83	120	4.583e-03
GO:BP	GO:0032964	collagen biosynthetic process	36	46	4.583e-03
GO:BP	GO:0001825	blastocyst formation	36	46	4.583e-03
GO:BP	GO:0042771	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	36	46	4.583e-03
GO:BP	GO:1900026	positive regulation of substrate adhesion-dependent cell spreading	34	43	4.588e-03
GO:BP	GO:0038084	vascular endothelial growth factor signaling pathway	34	43	4.588e-03
GO:BP	GO:0007492	endoderm development	63	88	4.780e-03
GO:BP	GO:0030301	cholesterol transport	73	104	4.835e-03
GO:BP	GO:0001678	intracellular glucose homeostasis	114	171	4.977e-03
GO:BP	GO:0061351	neural precursor cell proliferation	114	171	4.977e-03
GO:BP	GO:0010866	regulation of triglyceride biosynthetic process	18	20	5.049e-03
GO:BP	GO:0033137	negative regulation of peptidyl-serine phosphorylation	23	27	5.049e-03
GO:BP	GO:0071480	cellular response to gamma radiation	23	27	5.049e-03
GO:BP	GO:0009301	snRNA transcription	18	20	5.049e-03
GO:BP	GO:0090141	positive regulation of mitochondrial fission	18	20	5.049e-03
GO:BP	GO:0010614	negative regulation of cardiac muscle hypertrophy	23	27	5.049e-03
GO:BP	GO:0009648	photoperiodism	23	27	5.049e-03
GO:BP	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	18	20	5.049e-03
GO:BP	GO:1990182	exosomal secretion	18	20	5.049e-03
GO:BP	GO:0016188	synaptic vesicle maturation	23	27	5.049e-03
GO:BP	GO:0009251	glucan catabolic process	23	27	5.049e-03
GO:BP	GO:0055070	copper ion homeostasis	18	20	5.049e-03
GO:BP	GO:0061620	glycolytic process through glucose-6-phosphate	18	20	5.049e-03
GO:BP	GO:0032091	negative regulation of protein binding	47	63	5.091e-03
GO:BP	GO:0015918	sterol transport	76	109	5.170e-03
GO:BP	GO:0038061	non-canonical NF-kappaB signal transduction	84	122	5.285e-03
GO:BP	GO:0001706	endoderm formation	45	60	5.390e-03
GO:BP	GO:0003188	heart valve formation	15	16	5.439e-03
GO:BP	GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining	15	16	5.439e-03
GO:BP	GO:0030167	proteoglycan catabolic process	15	16	5.439e-03
GO:BP	GO:0036444	calcium import into the mitochondrion	15	16	5.439e-03
GO:BP	GO:0032897	negative regulation of viral transcription	15	16	5.439e-03
GO:BP	GO:0036260	RNA capping	15	16	5.439e-03
GO:BP	GO:2000725	regulation of cardiac muscle cell differentiation	15	16	5.439e-03
GO:BP	GO:1990166	protein localization to site of double-strand break	15	16	5.439e-03
GO:BP	GO:0098693	regulation of synaptic vesicle cycle	15	16	5.439e-03
GO:BP	GO:0016074	sno(s)RNA metabolic process	15	16	5.439e-03
GO:BP	GO:0110156	mRNA methylguanosine-cap decapping	15	16	5.439e-03
GO:BP	GO:0045637	regulation of myeloid cell differentiation	139	213	5.583e-03
GO:BP	GO:2000649	regulation of sodium ion transmembrane transporter activity	25	30	5.670e-03
GO:BP	GO:0032835	glomerulus development	52	71	5.670e-03
GO:BP	GO:0022011	myelination in peripheral nervous system	25	30	5.670e-03
GO:BP	GO:1900368	regulation of post-transcriptional gene silencing by regulatory ncRNA	25	30	5.670e-03
GO:BP	GO:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	25	30	5.670e-03
GO:BP	GO:2000629	negative regulation of miRNA metabolic process	25	30	5.670e-03
GO:BP	GO:0048668	collateral sprouting	25	30	5.670e-03
GO:BP	GO:0032292	peripheral nervous system axon ensheathment	25	30	5.670e-03
GO:BP	GO:0046683	response to organophosphorus	90	132	5.720e-03
GO:BP	GO:0072078	nephron tubule morphogenesis	57	79	6.047e-03
GO:BP	GO:0051149	positive regulation of muscle cell differentiation	50	68	6.081e-03
GO:BP	GO:0170033	L-amino acid metabolic process	116	175	6.107e-03
GO:BP	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	39	51	6.149e-03
GO:BP	GO:0010883	regulation of lipid storage	39	51	6.149e-03
GO:BP	GO:0060249	anatomical structure homeostasis	172	269	6.303e-03
GO:BP	GO:0042168	heme metabolic process	37	48	6.354e-03
GO:BP	GO:0006687	glycosphingolipid metabolic process	48	65	6.498e-03
GO:BP	GO:0046622	positive regulation of organ growth	35	45	6.498e-03
GO:BP	GO:0002931	response to ischemia	48	65	6.498e-03
GO:BP	GO:2000772	regulation of cellular senescence	35	45	6.498e-03
GO:BP	GO:1904063	negative regulation of cation transmembrane transport	55	76	6.533e-03
GO:BP	GO:0001941	postsynaptic membrane organization	33	42	6.542e-03
GO:BP	GO:0090181	regulation of cholesterol metabolic process	31	39	6.542e-03
GO:BP	GO:0015919	peroxisomal membrane transport	20	23	6.542e-03
GO:BP	GO:0009167	purine ribonucleoside monophosphate metabolic process	33	42	6.542e-03
GO:BP	GO:0099150	regulation of postsynaptic specialization assembly	20	23	6.542e-03
GO:BP	GO:0003180	aortic valve morphogenesis	31	39	6.542e-03
GO:BP	GO:0140112	extracellular vesicle biogenesis	20	23	6.542e-03
GO:BP	GO:0042307	positive regulation of protein import into nucleus	33	42	6.542e-03
GO:BP	GO:0043574	peroxisomal transport	20	23	6.542e-03
GO:BP	GO:0032401	establishment of melanosome localization	20	23	6.542e-03
GO:BP	GO:0046677	response to antibiotic	31	39	6.542e-03
GO:BP	GO:0002062	chondrocyte differentiation	83	121	6.626e-03
GO:BP	GO:0007009	plasma membrane organization	114	172	6.690e-03
GO:BP	GO:0006029	proteoglycan metabolic process	70	100	6.736e-03
GO:BP	GO:0001938	positive regulation of endothelial cell proliferation	65	92	6.807e-03
GO:BP	GO:0009161	ribonucleoside monophosphate metabolic process	46	62	6.894e-03
GO:BP	GO:0008347	glial cell migration	46	62	6.894e-03
GO:BP	GO:0002757	immune response-activating signaling pathway	303	494	7.048e-03
GO:BP	GO:1901654	response to ketone	148	229	7.058e-03
GO:BP	GO:1901605	alpha-amino acid metabolic process	139	214	7.279e-03
GO:BP	GO:0071887	leukocyte apoptotic process	81	118	7.287e-03
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	81	118	7.287e-03
GO:BP	GO:0072132	mesenchyme morphogenesis	44	59	7.323e-03
GO:BP	GO:0048678	response to axon injury	58	81	7.323e-03
GO:BP	GO:0072088	nephron epithelium morphogenesis	58	81	7.323e-03
GO:BP	GO:1904018	positive regulation of vasculature development	112	169	7.360e-03
GO:BP	GO:0001894	tissue homeostasis	171	268	7.376e-03
GO:BP	GO:0048857	neural nucleus development	51	70	7.570e-03
GO:BP	GO:0075522	IRES-dependent viral translational initiation	11	11	7.623e-03
GO:BP	GO:0090161	Golgi ribbon formation	11	11	7.623e-03
GO:BP	GO:2000178	negative regulation of neural precursor cell proliferation	22	26	7.623e-03
GO:BP	GO:2000050	regulation of non-canonical Wnt signaling pathway	22	26	7.623e-03
GO:BP	GO:0070213	protein auto-ADP-ribosylation	11	11	7.623e-03
GO:BP	GO:0036490	regulation of translation in response to endoplasmic reticulum stress	11	11	7.623e-03
GO:BP	GO:0044829	positive regulation by host of viral genome replication	11	11	7.623e-03
GO:BP	GO:0019081	viral translation	22	26	7.623e-03
GO:BP	GO:1905208	negative regulation of cardiocyte differentiation	11	11	7.623e-03
GO:BP	GO:0051469	vesicle fusion with vacuole	11	11	7.623e-03
GO:BP	GO:0007549	sex-chromosome dosage compensation	22	26	7.623e-03
GO:BP	GO:0072110	glomerular mesangial cell proliferation	11	11	7.623e-03
GO:BP	GO:0070198	protein localization to chromosome, telomeric region	22	26	7.623e-03
GO:BP	GO:1903564	regulation of protein localization to cilium	11	11	7.623e-03
GO:BP	GO:0071028	nuclear mRNA surveillance	11	11	7.623e-03
GO:BP	GO:0010613	positive regulation of cardiac muscle hypertrophy	22	26	7.623e-03
GO:BP	GO:0000338	protein deneddylation	11	11	7.623e-03
GO:BP	GO:0051036	regulation of endosome size	11	11	7.623e-03
GO:BP	GO:0006983	ER overload response	11	11	7.623e-03
GO:BP	GO:0062028	regulation of stress granule assembly	11	11	7.623e-03
GO:BP	GO:0006307	DNA alkylation repair	11	11	7.623e-03
GO:BP	GO:0061763	multivesicular body-lysosome fusion	11	11	7.623e-03
GO:BP	GO:0051875	pigment granule localization	22	26	7.623e-03
GO:BP	GO:0016185	synaptic vesicle budding from presynaptic endocytic zone membrane	11	11	7.623e-03
GO:BP	GO:1902547	regulation of cellular response to vascular endothelial growth factor stimulus	22	26	7.623e-03
GO:BP	GO:0071044	histone mRNA catabolic process	11	11	7.623e-03
GO:BP	GO:1903059	regulation of protein lipidation	11	11	7.623e-03
GO:BP	GO:0016479	negative regulation of transcription by RNA polymerase I	11	11	7.623e-03
GO:BP	GO:0022038	corpus callosum development	22	26	7.623e-03
GO:BP	GO:0006686	sphingomyelin biosynthetic process	11	11	7.623e-03
GO:BP	GO:0046324	regulation of D-glucose import	42	56	7.640e-03
GO:BP	GO:0002208	somatic diversification of immunoglobulins involved in immune response	42	56	7.640e-03
GO:BP	GO:0062237	protein localization to postsynapse	42	56	7.640e-03
GO:BP	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle	42	56	7.640e-03
GO:BP	GO:0002204	somatic recombination of immunoglobulin genes involved in immune response	42	56	7.640e-03
GO:BP	GO:0045190	isotype switching	42	56	7.640e-03
GO:BP	GO:0021761	limbic system development	87	128	7.752e-03
GO:BP	GO:0072080	nephron tubule development	71	102	7.781e-03
GO:BP	GO:0097194	execution phase of apoptosis	56	78	7.840e-03
GO:BP	GO:0006874	intracellular calcium ion homeostasis	192	304	7.854e-03
GO:BP	GO:0098696	regulation of neurotransmitter receptor localization to postsynaptic specialization membrane	17	19	7.972e-03
GO:BP	GO:0006491	N-glycan processing	17	19	7.972e-03
GO:BP	GO:0010558	negative regulation of macromolecule biosynthetic process	1570	2745	7.972e-03
GO:BP	GO:0097320	plasma membrane tubulation	17	19	7.972e-03
GO:BP	GO:1903830	magnesium ion transmembrane transport	17	19	7.972e-03
GO:BP	GO:0031053	primary miRNA processing	17	19	7.972e-03
GO:BP	GO:0032253	dense core granule localization	17	19	7.972e-03
GO:BP	GO:0090201	negative regulation of release of cytochrome c from mitochondria	17	19	7.972e-03
GO:BP	GO:0061158	3’-UTR-mediated mRNA destabilization	17	19	7.972e-03
GO:BP	GO:0003215	cardiac right ventricle morphogenesis	17	19	7.972e-03
GO:BP	GO:0034244	negative regulation of transcription elongation by RNA polymerase II	17	19	7.972e-03
GO:BP	GO:0035372	protein localization to microtubule	17	19	7.972e-03
GO:BP	GO:0060039	pericardium development	17	19	7.972e-03
GO:BP	GO:0001947	heart looping	49	67	7.982e-03
GO:BP	GO:0070050	neuron cellular homeostasis	49	67	7.982e-03
GO:BP	GO:0007584	response to nutrient	113	171	7.991e-03
GO:BP	GO:0030834	regulation of actin filament depolymerization	40	53	7.993e-03
GO:BP	GO:0086009	membrane repolarization	40	53	7.993e-03
GO:BP	GO:0034250	positive regulation of amide metabolic process	24	29	8.363e-03
GO:BP	GO:0099054	presynapse assembly	38	50	8.363e-03
GO:BP	GO:0060765	regulation of androgen receptor signaling pathway	24	29	8.363e-03
GO:BP	GO:0045668	negative regulation of osteoblast differentiation	38	50	8.363e-03
GO:BP	GO:0014741	negative regulation of muscle hypertrophy	24	29	8.363e-03
GO:BP	GO:0055023	positive regulation of cardiac muscle tissue growth	24	29	8.363e-03
GO:BP	GO:0043392	negative regulation of DNA binding	24	29	8.363e-03
GO:BP	GO:0060964	regulation of miRNA-mediated gene silencing	24	29	8.363e-03
GO:BP	GO:1903036	positive regulation of response to wounding	54	75	8.436e-03
GO:BP	GO:0009799	specification of symmetry	99	148	8.440e-03
GO:BP	GO:0009855	determination of bilateral symmetry	99	148	8.440e-03
GO:BP	GO:0051216	cartilage development	138	213	8.493e-03
GO:BP	GO:0032526	response to retinoic acid	77	112	8.601e-03
GO:BP	GO:0008306	associative learning	64	91	8.621e-03
GO:BP	GO:0033627	cell adhesion mediated by integrin	59	83	8.626e-03
GO:BP	GO:0071824	protein-DNA complex organization	167	262	8.638e-03
GO:BP	GO:0006308	DNA catabolic process	26	32	8.848e-03
GO:BP	GO:0016558	protein import into peroxisome matrix	14	15	8.848e-03
GO:BP	GO:0043248	proteasome assembly	14	15	8.848e-03
GO:BP	GO:2000052	positive regulation of non-canonical Wnt signaling pathway	14	15	8.848e-03
GO:BP	GO:0006620	post-translational protein targeting to endoplasmic reticulum membrane	14	15	8.848e-03
GO:BP	GO:0018231	peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine	14	15	8.848e-03
GO:BP	GO:0106057	negative regulation of calcineurin-mediated signaling	14	15	8.848e-03
GO:BP	GO:0018230	peptidyl-L-cysteine S-palmitoylation	14	15	8.848e-03
GO:BP	GO:0070986	left/right axis specification	14	15	8.848e-03
GO:BP	GO:0086069	bundle of His cell to Purkinje myocyte communication	14	15	8.848e-03
GO:BP	GO:0061684	chaperone-mediated autophagy	14	15	8.848e-03
GO:BP	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	14	15	8.848e-03
GO:BP	GO:0140042	lipid droplet formation	14	15	8.848e-03
GO:BP	GO:0071501	cellular response to sterol depletion	14	15	8.848e-03
GO:BP	GO:0061635	regulation of protein complex stability	14	15	8.848e-03
GO:BP	GO:0001936	regulation of endothelial cell proliferation	91	135	8.891e-03
GO:BP	GO:0009126	purine nucleoside monophosphate metabolic process	34	44	8.915e-03
GO:BP	GO:0061035	regulation of cartilage development	52	72	9.072e-03
GO:BP	GO:0045738	negative regulation of DNA repair	32	41	9.072e-03
GO:BP	GO:1904385	cellular response to angiotensin	28	35	9.072e-03
GO:BP	GO:1900744	regulation of p38MAPK cascade	32	41	9.072e-03
GO:BP	GO:0045746	negative regulation of Notch signaling pathway	32	41	9.072e-03
GO:BP	GO:0070302	regulation of stress-activated protein kinase signaling cascade	32	41	9.072e-03
GO:BP	GO:1901797	negative regulation of signal transduction by p53 class mediator	28	35	9.072e-03
GO:BP	GO:0061180	mammary gland epithelium development	52	72	9.072e-03
GO:BP	GO:0046320	regulation of fatty acid oxidation	28	35	9.072e-03
GO:BP	GO:0035904	aorta development	45	61	9.072e-03
GO:BP	GO:0035337	fatty-acyl-CoA metabolic process	32	41	9.072e-03
GO:BP	GO:0060043	regulation of cardiac muscle cell proliferation	30	38	9.137e-03
GO:BP	GO:0046473	phosphatidic acid metabolic process	30	38	9.137e-03
GO:BP	GO:0021955	central nervous system neuron axonogenesis	30	38	9.137e-03
GO:BP	GO:1903532	positive regulation of secretion by cell	188	298	9.187e-03
GO:BP	GO:0045787	positive regulation of cell cycle	219	351	9.230e-03
GO:BP	GO:0021549	cerebellum development	75	109	9.354e-03
GO:BP	GO:0015833	peptide transport	182	288	9.642e-03
GO:BP	GO:0007632	visual behavior	43	58	9.675e-03
GO:BP	GO:0070918	regulatory ncRNA processing	50	69	9.778e-03
GO:BP	GO:0052547	regulation of peptidase activity	50	69	9.778e-03
GO:BP	GO:0045947	negative regulation of translational initiation	19	22	9.924e-03
GO:BP	GO:0036120	cellular response to platelet-derived growth factor stimulus	19	22	9.924e-03
GO:BP	GO:0060314	regulation of ryanodine-sensitive calcium-release channel activity	19	22	9.924e-03
GO:BP	GO:0032482	Rab protein signal transduction	19	22	9.924e-03
GO:BP	GO:0032252	secretory granule localization	19	22	9.924e-03
GO:BP	GO:0035024	negative regulation of Rho protein signal transduction	19	22	9.924e-03
GO:BP	GO:0032402	melanosome transport	19	22	9.924e-03
GO:BP	GO:0032211	negative regulation of telomere maintenance via telomerase	19	22	9.924e-03
GO:BP	GO:0048593	camera-type eye morphogenesis	92	137	9.937e-03
GO:BP	GO:0022037	metencephalon development	81	119	1.012e-02
GO:BP	GO:1904019	epithelial cell apoptotic process	60	85	1.018e-02
GO:BP	GO:1903539	protein localization to postsynaptic membrane	41	55	1.026e-02
GO:BP	GO:0006778	porphyrin-containing compound metabolic process	41	55	1.026e-02
GO:BP	GO:0072009	nephron epithelium development	84	124	1.044e-02
GO:BP	GO:0006694	steroid biosynthetic process	110	167	1.054e-02
GO:BP	GO:1903169	regulation of calcium ion transmembrane transport	110	167	1.054e-02
GO:BP	GO:0048592	eye morphogenesis	113	172	1.054e-02
GO:BP	GO:0007052	mitotic spindle organization	90	134	1.096e-02
GO:BP	GO:0050878	regulation of body fluid levels	233	376	1.109e-02
GO:BP	GO:1901028	regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	21	25	1.142e-02
GO:BP	GO:1902455	negative regulation of stem cell population maintenance	21	25	1.142e-02
GO:BP	GO:2000209	regulation of anoikis	21	25	1.142e-02
GO:BP	GO:0097150	neuronal stem cell population maintenance	21	25	1.142e-02
GO:BP	GO:0060045	positive regulation of cardiac muscle cell proliferation	21	25	1.142e-02
GO:BP	GO:0046580	negative regulation of Ras protein signal transduction	21	25	1.142e-02
GO:BP	GO:0001919	regulation of receptor recycling	21	25	1.142e-02
GO:BP	GO:0048169	regulation of long-term neuronal synaptic plasticity	21	25	1.142e-02
GO:BP	GO:0062208	positive regulation of pattern recognition receptor signaling pathway	51	71	1.196e-02
GO:BP	GO:1902041	regulation of extrinsic apoptotic signaling pathway via death domain receptors	35	46	1.203e-02
GO:BP	GO:0071548	response to dexamethasone	35	46	1.203e-02
GO:BP	GO:0060761	negative regulation of response to cytokine stimulus	61	87	1.205e-02
GO:BP	GO:1901019	regulation of calcium ion transmembrane transporter activity	44	60	1.221e-02
GO:BP	GO:0002381	immunoglobulin production involved in immunoglobulin-mediated immune response	44	60	1.221e-02
GO:BP	GO:0043113	receptor clustering	44	60	1.221e-02
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	91	136	1.228e-02
GO:BP	GO:0071902	positive regulation of protein serine/threonine kinase activity	91	136	1.228e-02
GO:BP	GO:0046037	GMP metabolic process	23	28	1.237e-02
GO:BP	GO:0001573	ganglioside metabolic process	23	28	1.237e-02
GO:BP	GO:0010962	regulation of glucan biosynthetic process	23	28	1.237e-02
GO:BP	GO:0005979	regulation of glycogen biosynthetic process	23	28	1.237e-02
GO:BP	GO:0071549	cellular response to dexamethasone stimulus	23	28	1.237e-02
GO:BP	GO:0039529	RIG-I signaling pathway	23	28	1.237e-02
GO:BP	GO:1902894	negative regulation of miRNA transcription	23	28	1.237e-02
GO:BP	GO:1900745	positive regulation of p38MAPK cascade	23	28	1.237e-02
GO:BP	GO:2001259	positive regulation of cation channel activity	33	43	1.246e-02
GO:BP	GO:0007595	lactation	33	43	1.246e-02
GO:BP	GO:0051897	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	121	186	1.251e-02
GO:BP	GO:0044539	long-chain fatty acid import into cell	16	18	1.257e-02
GO:BP	GO:0061718	glucose catabolic process to pyruvate	16	18	1.257e-02
GO:BP	GO:0035973	aggrephagy	16	18	1.257e-02
GO:BP	GO:0071816	tail-anchored membrane protein insertion into ER membrane	16	18	1.257e-02
GO:BP	GO:0010042	response to manganese ion	16	18	1.257e-02
GO:BP	GO:0009208	pyrimidine ribonucleoside triphosphate metabolic process	16	18	1.257e-02
GO:BP	GO:0061621	canonical glycolysis	16	18	1.257e-02
GO:BP	GO:1900037	regulation of cellular response to hypoxia	16	18	1.257e-02
GO:BP	GO:0060977	coronary vasculature morphogenesis	16	18	1.257e-02
GO:BP	GO:0002573	myeloid leukocyte differentiation	153	240	1.266e-02
GO:BP	GO:0045766	positive regulation of angiogenesis	109	166	1.269e-02
GO:BP	GO:0090199	regulation of release of cytochrome c from mitochondria	31	40	1.278e-02
GO:BP	GO:0014911	positive regulation of smooth muscle cell migration	31	40	1.278e-02
GO:BP	GO:0043407	negative regulation of MAP kinase activity	31	40	1.278e-02
GO:BP	GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	31	40	1.278e-02
GO:BP	GO:0097107	postsynaptic density assembly	25	31	1.284e-02
GO:BP	GO:0061440	kidney vasculature development	25	31	1.284e-02
GO:BP	GO:0061437	renal system vasculature development	25	31	1.284e-02
GO:BP	GO:1904814	regulation of protein localization to chromosome, telomeric region	10	10	1.289e-02
GO:BP	GO:0070862	negative regulation of protein exit from endoplasmic reticulum	10	10	1.289e-02
GO:BP	GO:0034635	glutathione transport	10	10	1.289e-02
GO:BP	GO:0006625	protein targeting to peroxisome	10	10	1.289e-02
GO:BP	GO:1902966	positive regulation of protein localization to early endosome	10	10	1.289e-02
GO:BP	GO:0098884	postsynaptic neurotransmitter receptor internalization	27	34	1.289e-02
GO:BP	GO:0071166	ribonucleoprotein complex localization	10	10	1.289e-02
GO:BP	GO:0061626	pharyngeal arch artery morphogenesis	10	10	1.289e-02
GO:BP	GO:0060628	regulation of ER to Golgi vesicle-mediated transport	10	10	1.289e-02
GO:BP	GO:0070922	RISC complex assembly	10	10	1.289e-02
GO:BP	GO:0071425	hematopoietic stem cell proliferation	27	34	1.289e-02
GO:BP	GO:0101024	mitotic nuclear membrane organization	10	10	1.289e-02
GO:BP	GO:0070831	basement membrane assembly	10	10	1.289e-02
GO:BP	GO:0015820	L-leucine transport	10	10	1.289e-02
GO:BP	GO:1902965	regulation of protein localization to early endosome	10	10	1.289e-02
GO:BP	GO:0180012	co-transcriptional RNA 3’-end processing, cleavage and polyadenylation pathway	10	10	1.289e-02
GO:BP	GO:2000234	positive regulation of rRNA processing	10	10	1.289e-02
GO:BP	GO:0034332	adherens junction organization	42	57	1.289e-02
GO:BP	GO:0019673	GDP-mannose metabolic process	10	10	1.289e-02
GO:BP	GO:0032988	protein-RNA complex disassembly	10	10	1.289e-02
GO:BP	GO:0072124	regulation of glomerular mesangial cell proliferation	10	10	1.289e-02
GO:BP	GO:0010464	regulation of mesenchymal cell proliferation	27	34	1.289e-02
GO:BP	GO:0007084	mitotic nuclear membrane reassembly	10	10	1.289e-02
GO:BP	GO:0000492	box C/D snoRNP assembly	10	10	1.289e-02
GO:BP	GO:0051409	response to nitrosative stress	10	10	1.289e-02
GO:BP	GO:0140239	postsynaptic endocytosis	27	34	1.289e-02
GO:BP	GO:1904896	ESCRT complex disassembly	10	10	1.289e-02
GO:BP	GO:1902513	regulation of organelle transport along microtubule	10	10	1.289e-02
GO:BP	GO:0072089	stem cell proliferation	83	123	1.289e-02
GO:BP	GO:0031125	rRNA 3’-end processing	10	10	1.289e-02
GO:BP	GO:0003253	cardiac neural crest cell migration involved in outflow tract morphogenesis	10	10	1.289e-02
GO:BP	GO:1904903	ESCRT III complex disassembly	10	10	1.289e-02
GO:BP	GO:0006084	acetyl-CoA metabolic process	27	34	1.289e-02
GO:BP	GO:0010935	regulation of macrophage cytokine production	29	37	1.289e-02
GO:BP	GO:0048194	Golgi vesicle budding	10	10	1.289e-02
GO:BP	GO:0051292	nuclear pore complex assembly	10	10	1.289e-02
GO:BP	GO:1903242	regulation of cardiac muscle hypertrophy in response to stress	10	10	1.289e-02
GO:BP	GO:2000766	negative regulation of cytoplasmic translation	10	10	1.289e-02
GO:BP	GO:0010612	regulation of cardiac muscle adaptation	10	10	1.289e-02
GO:BP	GO:2000756	regulation of peptidyl-lysine acetylation	10	10	1.289e-02
GO:BP	GO:0015937	coenzyme A biosynthetic process	10	10	1.289e-02
GO:BP	GO:0006283	transcription-coupled nucleotide-excision repair	10	10	1.289e-02
GO:BP	GO:1901838	positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	10	10	1.289e-02
GO:BP	GO:0034142	toll-like receptor 4 signaling pathway	42	57	1.289e-02
GO:BP	GO:0010934	macrophage cytokine production	29	37	1.289e-02
GO:BP	GO:0051047	positive regulation of secretion	201	322	1.292e-02
GO:BP	GO:0050796	regulation of insulin secretion	116	178	1.357e-02
GO:BP	GO:0048260	positive regulation of receptor-mediated endocytosis	40	54	1.366e-02
GO:BP	GO:0045599	negative regulation of fat cell differentiation	40	54	1.366e-02
GO:BP	GO:0072348	sulfur compound transport	47	65	1.369e-02
GO:BP	GO:1990173	protein localization to nucleoplasm	13	14	1.428e-02
GO:BP	GO:0051127	positive regulation of actin nucleation	13	14	1.428e-02
GO:BP	GO:0019852	L-ascorbic acid metabolic process	13	14	1.428e-02
GO:BP	GO:0001921	positive regulation of receptor recycling	13	14	1.428e-02
GO:BP	GO:0051924	regulation of calcium ion transport	155	244	1.428e-02
GO:BP	GO:0051775	response to redox state	13	14	1.428e-02
GO:BP	GO:0061430	bone trabecula morphogenesis	13	14	1.428e-02
GO:BP	GO:0015780	nucleotide-sugar transmembrane transport	13	14	1.428e-02
GO:BP	GO:0010763	positive regulation of fibroblast migration	13	14	1.428e-02
GO:BP	GO:0042983	amyloid precursor protein biosynthetic process	13	14	1.428e-02
GO:BP	GO:0015803	branched-chain amino acid transport	13	14	1.428e-02
GO:BP	GO:0042984	regulation of amyloid precursor protein biosynthetic process	13	14	1.428e-02
GO:BP	GO:0097468	programmed cell death in response to reactive oxygen species	13	14	1.428e-02
GO:BP	GO:0048388	endosomal lumen acidification	13	14	1.428e-02
GO:BP	GO:0030497	fatty acid elongation	13	14	1.428e-02
GO:BP	GO:0060816	random inactivation of X chromosome	13	14	1.428e-02
GO:BP	GO:2000095	regulation of Wnt signaling pathway, planar cell polarity pathway	13	14	1.428e-02
GO:BP	GO:0043517	positive regulation of DNA damage response, signal transduction by p53 class mediator	13	14	1.428e-02
GO:BP	GO:0043144	sno(s)RNA processing	13	14	1.428e-02
GO:BP	GO:0010635	regulation of mitochondrial fusion	13	14	1.428e-02
GO:BP	GO:0008542	visual learning	38	51	1.448e-02
GO:BP	GO:0048013	ephrin receptor signaling pathway	38	51	1.448e-02
GO:BP	GO:0030168	platelet activation	93	140	1.483e-02
GO:BP	GO:0008277	regulation of G protein-coupled receptor signaling pathway	102	155	1.496e-02
GO:BP	GO:0060216	definitive hemopoiesis	18	21	1.496e-02
GO:BP	GO:1902284	neuron projection extension involved in neuron projection guidance	18	21	1.496e-02
GO:BP	GO:0010566	regulation of ketone biosynthetic process	18	21	1.496e-02
GO:BP	GO:0071322	cellular response to carbohydrate stimulus	108	165	1.496e-02
GO:BP	GO:0036498	IRE1-mediated unfolded protein response	18	21	1.496e-02
GO:BP	GO:0140354	lipid import into cell	18	21	1.496e-02
GO:BP	GO:0072111	cell proliferation involved in kidney development	18	21	1.496e-02
GO:BP	GO:0086012	membrane depolarization during cardiac muscle cell action potential	18	21	1.496e-02
GO:BP	GO:0098760	response to interleukin-7	18	21	1.496e-02
GO:BP	GO:0016556	mRNA modification	18	21	1.496e-02
GO:BP	GO:0097734	extracellular exosome biogenesis	18	21	1.496e-02
GO:BP	GO:0097062	dendritic spine maintenance	18	21	1.496e-02
GO:BP	GO:0009067	aspartate family amino acid biosynthetic process	18	21	1.496e-02
GO:BP	GO:0140896	cGAS/STING signaling pathway	18	21	1.496e-02
GO:BP	GO:2001135	regulation of endocytic recycling	18	21	1.496e-02
GO:BP	GO:0048846	axon extension involved in axon guidance	18	21	1.496e-02
GO:BP	GO:0046426	negative regulation of receptor signaling pathway via JAK-STAT	18	21	1.496e-02
GO:BP	GO:0034764	positive regulation of transmembrane transport	130	202	1.520e-02
GO:BP	GO:0071277	cellular response to calcium ion	55	78	1.524e-02
GO:BP	GO:0021575	hindbrain morphogenesis	36	48	1.528e-02
GO:BP	GO:0018212	peptidyl-tyrosine modification	153	241	1.549e-02
GO:BP	GO:0002683	negative regulation of immune system process	312	515	1.553e-02
GO:BP	GO:0015807	L-amino acid transport	63	91	1.590e-02
GO:BP	GO:0061458	reproductive system development	198	318	1.604e-02
GO:BP	GO:0097237	cellular response to toxic substance	88	132	1.609e-02
GO:BP	GO:0021587	cerebellum morphogenesis	34	45	1.613e-02
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	34	45	1.613e-02
GO:BP	GO:0007596	blood coagulation	147	231	1.614e-02
GO:BP	GO:0001508	action potential	112	172	1.623e-02
GO:BP	GO:0009048	dosage compensation by inactivation of X chromosome	20	24	1.677e-02
GO:BP	GO:1904889	regulation of excitatory synapse assembly	20	24	1.677e-02
GO:BP	GO:1900746	regulation of vascular endothelial growth factor signaling pathway	20	24	1.677e-02
GO:BP	GO:0008334	histone mRNA metabolic process	20	24	1.677e-02
GO:BP	GO:0061615	glycolytic process through fructose-6-phosphate	20	24	1.677e-02
GO:BP	GO:0061484	hematopoietic stem cell homeostasis	20	24	1.677e-02
GO:BP	GO:0051905	establishment of pigment granule localization	20	24	1.677e-02
GO:BP	GO:0070296	sarcoplasmic reticulum calcium ion transport	32	42	1.688e-02
GO:BP	GO:0032728	positive regulation of interferon-beta production	32	42	1.688e-02
GO:BP	GO:1990776	response to angiotensin	32	42	1.688e-02
GO:BP	GO:0007599	hemostasis	151	238	1.690e-02
GO:BP	GO:0045191	regulation of isotype switching	30	39	1.754e-02
GO:BP	GO:0010591	regulation of lamellipodium assembly	30	39	1.754e-02
GO:BP	GO:0070884	regulation of calcineurin-NFAT signaling cascade	30	39	1.754e-02
GO:BP	GO:1905476	negative regulation of protein localization to membrane	30	39	1.754e-02
GO:BP	GO:2000780	negative regulation of double-strand break repair	30	39	1.754e-02
GO:BP	GO:0099622	cardiac muscle cell membrane repolarization	30	39	1.754e-02
GO:BP	GO:0032872	regulation of stress-activated MAPK cascade	30	39	1.754e-02
GO:BP	GO:0014742	positive regulation of muscle hypertrophy	22	27	1.781e-02
GO:BP	GO:0060343	trabecula formation	22	27	1.781e-02
GO:BP	GO:0044827	modulation by host of viral genome replication	22	27	1.781e-02
GO:BP	GO:0032878	regulation of establishment or maintenance of cell polarity	22	27	1.781e-02
GO:BP	GO:0006638	neutral lipid metabolic process	89	134	1.783e-02
GO:BP	GO:0051208	sequestering of calcium ion	89	134	1.783e-02
GO:BP	GO:0097484	dendrite extension	28	36	1.803e-02
GO:BP	GO:0060218	hematopoietic stem cell differentiation	28	36	1.803e-02
GO:BP	GO:0017145	stem cell division	28	36	1.803e-02
GO:BP	GO:0055074	calcium ion homeostasis	204	329	1.821e-02
GO:BP	GO:2001222	regulation of neuron migration	39	53	1.825e-02
GO:BP	GO:0099170	postsynaptic modulation of chemical synaptic transmission	26	33	1.826e-02
GO:BP	GO:0051642	centrosome localization	26	33	1.826e-02
GO:BP	GO:0061842	microtubule organizing center localization	26	33	1.826e-02
GO:BP	GO:0061384	heart trabecula morphogenesis	26	33	1.826e-02
GO:BP	GO:0015012	heparan sulfate proteoglycan biosynthetic process	26	33	1.826e-02
GO:BP	GO:0001736	establishment of planar polarity	26	33	1.826e-02
GO:BP	GO:0045648	positive regulation of erythrocyte differentiation	24	30	1.826e-02
GO:BP	GO:0007164	establishment of tissue polarity	26	33	1.826e-02
GO:BP	GO:1902807	negative regulation of cell cycle G1/S phase transition	44	61	1.939e-02
GO:BP	GO:0032102	negative regulation of response to external stimulus	238	388	1.939e-02
GO:BP	GO:0090083	regulation of inclusion body assembly	15	17	1.939e-02
GO:BP	GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity	15	17	1.939e-02
GO:BP	GO:0019184	nonribosomal peptide biosynthetic process	15	17	1.939e-02
GO:BP	GO:1901096	regulation of autophagosome maturation	15	17	1.939e-02
GO:BP	GO:0006878	intracellular copper ion homeostasis	15	17	1.939e-02
GO:BP	GO:1903541	regulation of exosomal secretion	15	17	1.939e-02
GO:BP	GO:0033151	V(D)J recombination	15	17	1.939e-02
GO:BP	GO:0043217	myelin maintenance	15	17	1.939e-02
GO:BP	GO:1902165	regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	15	17	1.939e-02
GO:BP	GO:0071895	odontoblast differentiation	15	17	1.939e-02
GO:BP	GO:0018126	protein hydroxylation	15	17	1.939e-02
GO:BP	GO:0099638	endosome to plasma membrane protein transport	15	17	1.939e-02
GO:BP	GO:0046365	monosaccharide catabolic process	37	50	1.946e-02
GO:BP	GO:0014902	myotube differentiation	87	131	1.954e-02
GO:BP	GO:1901657	glycosyl compound metabolic process	54	77	1.954e-02
GO:BP	GO:0033363	secretory granule organization	49	69	1.970e-02
GO:BP	GO:0048608	reproductive structure development	195	314	1.979e-02
GO:BP	GO:0045055	regulated exocytosis	147	232	2.007e-02
GO:BP	GO:0170039	proteinogenic amino acid metabolic process	115	178	2.077e-02
GO:BP	GO:0006509	membrane protein ectodomain proteolysis	35	47	2.079e-02
GO:BP	GO:0060711	labyrinthine layer development	35	47	2.079e-02
GO:BP	GO:0002521	leukocyte differentiation	380	636	2.085e-02
GO:BP	GO:0048168	regulation of neuronal synaptic plasticity	42	58	2.094e-02
GO:BP	GO:0046148	pigment biosynthetic process	42	58	2.094e-02
GO:BP	GO:0007389	pattern specification process	289	477	2.094e-02
GO:BP	GO:0018108	peptidyl-tyrosine phosphorylation	151	239	2.094e-02
GO:BP	GO:0045814	negative regulation of gene expression, epigenetic	128	200	2.109e-02
GO:BP	GO:0046660	female sex differentiation	82	123	2.132e-02
GO:BP	GO:0014855	striated muscle cell proliferation	52	74	2.141e-02
GO:BP	GO:0021885	forebrain cell migration	47	66	2.150e-02
GO:BP	GO:0030282	bone mineralization	85	128	2.152e-02
GO:BP	GO:0071331	cellular response to hexose stimulus	100	153	2.164e-02
GO:BP	GO:0006639	acylglycerol metabolic process	88	133	2.165e-02
GO:BP	GO:0032881	regulation of polysaccharide metabolic process	33	44	2.204e-02
GO:BP	GO:1903170	negative regulation of calcium ion transmembrane transport	33	44	2.204e-02
GO:BP	GO:0048285	organelle fission	302	500	2.204e-02
GO:BP	GO:0070900	mitochondrial tRNA modification	9	9	2.213e-02
GO:BP	GO:0035520	monoubiquitinated protein deubiquitination	9	9	2.213e-02
GO:BP	GO:0140673	transcription elongation-coupled chromatin remodeling	9	9	2.213e-02
GO:BP	GO:0007021	tubulin complex assembly	9	9	2.213e-02
GO:BP	GO:0003162	atrioventricular node development	9	9	2.213e-02
GO:BP	GO:0062176	R-loop processing	9	9	2.213e-02
GO:BP	GO:0036500	ATF6-mediated unfolded protein response	9	9	2.213e-02
GO:BP	GO:0042532	negative regulation of tyrosine phosphorylation of STAT protein	9	9	2.213e-02
GO:BP	GO:1904153	negative regulation of retrograde protein transport, ER to cytosol	9	9	2.213e-02
GO:BP	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	9	9	2.213e-02
GO:BP	GO:0042796	snRNA transcription by RNA polymerase III	9	9	2.213e-02
GO:BP	GO:0000467	exonucleolytic trimming to generate mature 3’-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	9	9	2.213e-02
GO:BP	GO:0031440	regulation of mRNA 3’-end processing	9	9	2.213e-02
GO:BP	GO:0034214	protein hexamerization	9	9	2.213e-02
GO:BP	GO:0090522	vesicle tethering involved in exocytosis	9	9	2.213e-02
GO:BP	GO:0006449	regulation of translational termination	9	9	2.213e-02
GO:BP	GO:2000197	regulation of ribonucleoprotein complex localization	9	9	2.213e-02
GO:BP	GO:2000169	regulation of peptidyl-cysteine S-nitrosylation	9	9	2.213e-02
GO:BP	GO:0000447	endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	9	9	2.213e-02
GO:BP	GO:0097680	double-strand break repair via classical nonhomologous end joining	9	9	2.213e-02
GO:BP	GO:2000096	positive regulation of Wnt signaling pathway, planar cell polarity pathway	9	9	2.213e-02
GO:BP	GO:0030200	heparan sulfate proteoglycan catabolic process	9	9	2.213e-02
GO:BP	GO:0000301	retrograde transport, vesicle recycling within Golgi	9	9	2.213e-02
GO:BP	GO:0180010	co-transcriptional mRNA 3’-end processing, cleavage and polyadenylation pathway	9	9	2.213e-02
GO:BP	GO:1990481	mRNA pseudouridine synthesis	9	9	2.213e-02
GO:BP	GO:1903332	regulation of protein folding	9	9	2.213e-02
GO:BP	GO:0160063	multi-pass transmembrane protein insertion into ER membrane	9	9	2.213e-02
GO:BP	GO:0016926	protein desumoylation	9	9	2.213e-02
GO:BP	GO:0031946	regulation of glucocorticoid biosynthetic process	9	9	2.213e-02
GO:BP	GO:1900864	mitochondrial RNA modification	9	9	2.213e-02
GO:BP	GO:0048034	heme O biosynthetic process	9	9	2.213e-02
GO:BP	GO:0090119	vesicle-mediated cholesterol transport	9	9	2.213e-02
GO:BP	GO:1901030	positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway	9	9	2.213e-02
GO:BP	GO:0048033	heme O metabolic process	9	9	2.213e-02
GO:BP	GO:1904874	positive regulation of telomerase RNA localization to Cajal body	9	9	2.213e-02
GO:BP	GO:0034085	establishment of sister chromatid cohesion	9	9	2.213e-02
GO:BP	GO:0110076	negative regulation of ferroptosis	9	9	2.213e-02
GO:BP	GO:0010998	regulation of translational initiation by eIF2 alpha phosphorylation	9	9	2.213e-02
GO:BP	GO:0048771	tissue remodeling	116	180	2.215e-02
GO:BP	GO:0032410	negative regulation of transporter activity	40	55	2.232e-02
GO:BP	GO:0006220	pyrimidine nucleotide metabolic process	40	55	2.232e-02
GO:BP	GO:0070555	response to interleukin-1	74	110	2.245e-02
GO:BP	GO:2001044	regulation of integrin-mediated signaling pathway	17	20	2.259e-02
GO:BP	GO:0046827	positive regulation of protein export from nucleus	17	20	2.259e-02
GO:BP	GO:0098761	cellular response to interleukin-7	17	20	2.259e-02
GO:BP	GO:0015693	magnesium ion transport	17	20	2.259e-02
GO:BP	GO:2001224	positive regulation of neuron migration	17	20	2.259e-02
GO:BP	GO:0060973	cell migration involved in heart development	17	20	2.259e-02
GO:BP	GO:0010421	hydrogen peroxide-mediated programmed cell death	12	13	2.285e-02
GO:BP	GO:0046349	amino sugar biosynthetic process	12	13	2.285e-02
GO:BP	GO:0045793	positive regulation of cell size	12	13	2.285e-02
GO:BP	GO:1902902	negative regulation of autophagosome assembly	12	13	2.285e-02
GO:BP	GO:0140588	chromatin looping	12	13	2.285e-02
GO:BP	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	12	13	2.285e-02
GO:BP	GO:0042761	very long-chain fatty acid biosynthetic process	12	13	2.285e-02
GO:BP	GO:0006054	N-acetylneuraminate metabolic process	12	13	2.285e-02
GO:BP	GO:0034498	early endosome to Golgi transport	12	13	2.285e-02
GO:BP	GO:0071233	cellular response to L-leucine	12	13	2.285e-02
GO:BP	GO:0006167	AMP biosynthetic process	12	13	2.285e-02
GO:BP	GO:0034982	mitochondrial protein processing	12	13	2.285e-02
GO:BP	GO:0032486	Rap protein signal transduction	12	13	2.285e-02
GO:BP	GO:0031987	locomotion involved in locomotory behavior	12	13	2.285e-02
GO:BP	GO:0031571	mitotic G1 DNA damage checkpoint signaling	12	13	2.285e-02
GO:BP	GO:0090481	pyrimidine nucleotide-sugar transmembrane transport	12	13	2.285e-02
GO:BP	GO:0071679	commissural neuron axon guidance	12	13	2.285e-02
GO:BP	GO:0006361	transcription initiation at RNA polymerase I promoter	12	13	2.285e-02
GO:BP	GO:0070142	synaptic vesicle budding	12	13	2.285e-02
GO:BP	GO:0098935	dendritic transport	12	13	2.285e-02
GO:BP	GO:0061097	regulation of protein tyrosine kinase activity	31	41	2.285e-02
GO:BP	GO:0042559	pteridine-containing compound biosynthetic process	12	13	2.285e-02
GO:BP	GO:0038203	TORC2 signaling	12	13	2.285e-02
GO:BP	GO:0061668	mitochondrial ribosome assembly	12	13	2.285e-02
GO:BP	GO:0022029	telencephalon cell migration	45	63	2.288e-02
GO:BP	GO:0043406	positive regulation of MAP kinase activity	50	71	2.288e-02
GO:BP	GO:0071326	cellular response to monosaccharide stimulus	101	155	2.311e-02
GO:BP	GO:0050714	positive regulation of protein secretion	98	150	2.324e-02
GO:BP	GO:0071333	cellular response to glucose stimulus	98	150	2.324e-02
GO:BP	GO:0050817	coagulation	150	238	2.381e-02
GO:BP	GO:0045880	positive regulation of smoothened signaling pathway	29	38	2.382e-02
GO:BP	GO:0043243	positive regulation of protein-containing complex disassembly	29	38	2.382e-02
GO:BP	GO:1904707	positive regulation of vascular associated smooth muscle cell proliferation	29	38	2.382e-02
GO:BP	GO:0010799	regulation of peptidyl-threonine phosphorylation	29	38	2.382e-02
GO:BP	GO:0021696	cerebellar cortex morphogenesis	29	38	2.382e-02
GO:BP	GO:1900181	negative regulation of protein localization to nucleus	29	38	2.382e-02
GO:BP	GO:0048536	spleen development	29	38	2.382e-02
GO:BP	GO:0001836	release of cytochrome c from mitochondria	38	52	2.382e-02
GO:BP	GO:0034109	homotypic cell-cell adhesion	69	102	2.390e-02
GO:BP	GO:0031349	positive regulation of defense response	305	506	2.398e-02
GO:BP	GO:0106118	regulation of sterol biosynthetic process	19	23	2.438e-02
GO:BP	GO:0046823	negative regulation of nucleocytoplasmic transport	19	23	2.438e-02
GO:BP	GO:1905874	regulation of postsynaptic density organization	19	23	2.438e-02
GO:BP	GO:0051904	pigment granule transport	19	23	2.438e-02
GO:BP	GO:0060339	negative regulation of type I interferon-mediated signaling pathway	19	23	2.438e-02
GO:BP	GO:0003177	pulmonary valve development	19	23	2.438e-02
GO:BP	GO:0045540	regulation of cholesterol biosynthetic process	19	23	2.438e-02
GO:BP	GO:0060392	negative regulation of SMAD protein signal transduction	19	23	2.438e-02
GO:BP	GO:0038128	ERBB2 signaling pathway	19	23	2.438e-02
GO:BP	GO:0010640	regulation of platelet-derived growth factor receptor signaling pathway	19	23	2.438e-02
GO:BP	GO:0060444	branching involved in mammary gland duct morphogenesis	19	23	2.438e-02
GO:BP	GO:0010878	cholesterol storage	19	23	2.438e-02
GO:BP	GO:0006081	aldehyde metabolic process	53	76	2.440e-02
GO:BP	GO:0090307	mitotic spindle assembly	53	76	2.440e-02
GO:BP	GO:0000038	very long-chain fatty acid metabolic process	27	35	2.466e-02
GO:BP	GO:1902410	mitotic cytokinetic process	27	35	2.466e-02
GO:BP	GO:0002684	positive regulation of immune system process	641	1099	2.521e-02
GO:BP	GO:0002026	regulation of the force of heart contraction	21	26	2.531e-02
GO:BP	GO:1990748	cellular detoxification	81	122	2.531e-02
GO:BP	GO:0006760	folic acid-containing compound metabolic process	21	26	2.531e-02
GO:BP	GO:0019985	translesion synthesis	21	26	2.531e-02
GO:BP	GO:0046339	diacylglycerol metabolic process	21	26	2.531e-02
GO:BP	GO:0071684	organism emergence from protective structure	21	26	2.531e-02
GO:BP	GO:0035313	wound healing, spreading of epidermal cells	21	26	2.531e-02
GO:BP	GO:0035188	hatching	21	26	2.531e-02
GO:BP	GO:2000737	negative regulation of stem cell differentiation	21	26	2.531e-02
GO:BP	GO:0071108	protein K48-linked deubiquitination	25	32	2.531e-02
GO:BP	GO:0006007	glucose catabolic process	21	26	2.531e-02
GO:BP	GO:0001835	blastocyst hatching	21	26	2.531e-02
GO:BP	GO:0046716	muscle cell cellular homeostasis	21	26	2.531e-02
GO:BP	GO:0061028	establishment of endothelial barrier	36	49	2.546e-02
GO:BP	GO:0072012	glomerulus vasculature development	23	29	2.553e-02
GO:BP	GO:0000272	polysaccharide catabolic process	23	29	2.553e-02
GO:BP	GO:0021680	cerebellar Purkinje cell layer development	23	29	2.553e-02
GO:BP	GO:0010165	response to X-ray	23	29	2.553e-02
GO:BP	GO:0035767	endothelial cell chemotaxis	23	29	2.553e-02
GO:BP	GO:0051279	regulation of release of sequestered calcium ion into cytosol	56	81	2.571e-02
GO:BP	GO:0030166	proteoglycan biosynthetic process	51	73	2.671e-02
GO:BP	GO:0032963	collagen metabolic process	70	104	2.677e-02
GO:BP	GO:0006826	iron ion transport	41	57	2.684e-02
GO:BP	GO:0051055	negative regulation of lipid biosynthetic process	41	57	2.684e-02
GO:BP	GO:0098900	regulation of action potential	41	57	2.684e-02
GO:BP	GO:0033173	calcineurin-NFAT signaling cascade	34	46	2.731e-02
GO:BP	GO:1900271	regulation of long-term synaptic potentiation	34	46	2.731e-02
GO:BP	GO:0019320	hexose catabolic process	34	46	2.731e-02
GO:BP	GO:0003016	respiratory system process	34	46	2.731e-02
GO:BP	GO:0009410	response to xenobiotic stimulus	266	439	2.749e-02
GO:BP	GO:0001775	cell activation	659	1132	2.761e-02
GO:BP	GO:0002790	peptide secretion	163	261	2.767e-02
GO:BP	GO:0021953	central nervous system neuron differentiation	136	215	2.833e-02
GO:BP	GO:0006816	calcium ion transport	263	434	2.844e-02
GO:BP	GO:0070371	ERK1 and ERK2 cascade	185	299	2.887e-02
GO:BP	GO:0043647	inositol phosphate metabolic process	32	43	2.925e-02
GO:BP	GO:0030866	cortical actin cytoskeleton organization	32	43	2.925e-02
GO:BP	GO:0072171	mesonephric tubule morphogenesis	49	70	2.930e-02
GO:BP	GO:0035773	insulin secretion involved in cellular response to glucose stimulus	49	70	2.930e-02
GO:BP	GO:0051302	regulation of cell division	120	188	2.942e-02
GO:BP	GO:0120162	positive regulation of cold-induced thermogenesis	68	101	2.951e-02
GO:BP	GO:0001732	formation of cytoplasmic translation initiation complex	14	16	2.954e-02
GO:BP	GO:0031054	pre-miRNA processing	14	16	2.954e-02
GO:BP	GO:0031269	pseudopodium assembly	14	16	2.954e-02
GO:BP	GO:1902307	positive regulation of sodium ion transmembrane transport	14	16	2.954e-02
GO:BP	GO:0097009	energy homeostasis	57	83	2.954e-02
GO:BP	GO:0046036	CTP metabolic process	14	16	2.954e-02
GO:BP	GO:0072109	glomerular mesangium development	14	16	2.954e-02
GO:BP	GO:0006825	copper ion transport	14	16	2.954e-02
GO:BP	GO:0010633	negative regulation of epithelial cell migration	14	16	2.954e-02
GO:BP	GO:0072350	tricarboxylic acid metabolic process	14	16	2.954e-02
GO:BP	GO:0016078	tRNA decay	14	16	2.954e-02
GO:BP	GO:0042795	snRNA transcription by RNA polymerase II	14	16	2.954e-02
GO:BP	GO:1905906	regulation of amyloid fibril formation	14	16	2.954e-02
GO:BP	GO:0098877	neurotransmitter receptor transport to plasma membrane	14	16	2.954e-02
GO:BP	GO:1904754	positive regulation of vascular associated smooth muscle cell migration	14	16	2.954e-02
GO:BP	GO:0043201	response to L-leucine	14	16	2.954e-02
GO:BP	GO:0001960	negative regulation of cytokine-mediated signaling pathway	57	83	2.954e-02
GO:BP	GO:0030033	microvillus assembly	14	16	2.954e-02
GO:BP	GO:0044849	estrous cycle	14	16	2.954e-02
GO:BP	GO:1901526	positive regulation of mitophagy	14	16	2.954e-02
GO:BP	GO:0046753	non-lytic viral release	14	16	2.954e-02
GO:BP	GO:0045824	negative regulation of innate immune response	60	88	3.069e-02
GO:BP	GO:0002832	negative regulation of response to biotic stimulus	80	121	3.070e-02
GO:BP	GO:0032355	response to estradiol	80	121	3.070e-02
GO:BP	GO:0098739	import across plasma membrane	124	195	3.077e-02
GO:BP	GO:0106056	regulation of calcineurin-mediated signaling	30	40	3.092e-02
GO:BP	GO:0072337	modified amino acid transport	30	40	3.092e-02
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	52	75	3.093e-02
GO:BP	GO:0051048	negative regulation of secretion	108	168	3.134e-02
GO:BP	GO:0031297	replication fork processing	37	51	3.142e-02
GO:BP	GO:0035987	endodermal cell differentiation	37	51	3.142e-02
GO:BP	GO:0001656	metanephros development	63	93	3.158e-02
GO:BP	GO:0035019	somatic stem cell population maintenance	47	67	3.194e-02
GO:BP	GO:0030514	negative regulation of BMP signaling pathway	42	59	3.222e-02
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	42	59	3.222e-02
GO:BP	GO:0045921	positive regulation of exocytosis	55	80	3.249e-02
GO:BP	GO:0030072	peptide hormone secretion	159	255	3.261e-02
GO:BP	GO:1900225	regulation of NLRP3 inflammasome complex assembly	28	37	3.267e-02
GO:BP	GO:0031076	embryonic camera-type eye development	28	37	3.267e-02
GO:BP	GO:0010874	regulation of cholesterol efflux	28	37	3.267e-02
GO:BP	GO:0051154	negative regulation of striated muscle cell differentiation	28	37	3.267e-02
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	28	37	3.267e-02
GO:BP	GO:1903531	negative regulation of secretion by cell	96	148	3.296e-02
GO:BP	GO:0046879	hormone secretion	199	324	3.333e-02
GO:BP	GO:0003184	pulmonary valve morphogenesis	16	19	3.363e-02
GO:BP	GO:0061099	negative regulation of protein tyrosine kinase activity	16	19	3.363e-02
GO:BP	GO:0070525	tRNA threonylcarbamoyladenosine metabolic process	16	19	3.363e-02
GO:BP	GO:1904030	negative regulation of cyclin-dependent protein kinase activity	16	19	3.363e-02
GO:BP	GO:0006766	vitamin metabolic process	78	118	3.363e-02
GO:BP	GO:0006857	oligopeptide transport	16	19	3.363e-02
GO:BP	GO:0043171	peptide catabolic process	16	19	3.363e-02
GO:BP	GO:0007162	negative regulation of cell adhesion	181	293	3.363e-02
GO:BP	GO:0097401	synaptic vesicle lumen acidification	16	19	3.363e-02
GO:BP	GO:0009163	nucleoside biosynthetic process	16	19	3.363e-02
GO:BP	GO:0034404	nucleobase-containing small molecule biosynthetic process	16	19	3.363e-02
GO:BP	GO:1903599	positive regulation of autophagy of mitochondrion	16	19	3.363e-02
GO:BP	GO:0034260	negative regulation of GTPase activity	16	19	3.363e-02
GO:BP	GO:0099151	regulation of postsynaptic density assembly	16	19	3.363e-02
GO:BP	GO:0048268	clathrin coat assembly	16	19	3.363e-02
GO:BP	GO:1902004	positive regulation of amyloid-beta formation	16	19	3.363e-02
GO:BP	GO:0031644	regulation of nervous system process	78	118	3.363e-02
GO:BP	GO:2000811	negative regulation of anoikis	16	19	3.363e-02
GO:BP	GO:0048311	mitochondrion distribution	16	19	3.363e-02
GO:BP	GO:0006607	NLS-bearing protein import into nucleus	16	19	3.363e-02
GO:BP	GO:0030278	regulation of ossification	81	123	3.364e-02
GO:BP	GO:0007435	salivary gland morphogenesis	26	34	3.407e-02
GO:BP	GO:0032373	positive regulation of sterol transport	26	34	3.407e-02
GO:BP	GO:0061081	positive regulation of myeloid leukocyte cytokine production involved in immune response	26	34	3.407e-02
GO:BP	GO:0006536	glutamate metabolic process	26	34	3.407e-02
GO:BP	GO:0019674	NAD metabolic process	26	34	3.407e-02
GO:BP	GO:0032376	positive regulation of cholesterol transport	26	34	3.407e-02
GO:BP	GO:0051965	positive regulation of synapse assembly	45	64	3.476e-02
GO:BP	GO:0045807	positive regulation of endocytosis	100	155	3.517e-02
GO:BP	GO:0009636	response to toxic substance	157	252	3.522e-02
GO:BP	GO:0034311	diol metabolic process	24	31	3.541e-02
GO:BP	GO:0032232	negative regulation of actin filament bundle assembly	24	31	3.541e-02
GO:BP	GO:0045070	positive regulation of viral genome replication	24	31	3.541e-02
GO:BP	GO:1900027	regulation of ruffle assembly	24	31	3.541e-02
GO:BP	GO:0010458	exit from mitosis	24	31	3.541e-02
GO:BP	GO:0007064	mitotic sister chromatid cohesion	24	31	3.541e-02
GO:BP	GO:0070588	calcium ion transmembrane transport	208	340	3.555e-02
GO:BP	GO:1900273	positive regulation of long-term synaptic potentiation	18	22	3.567e-02
GO:BP	GO:0016082	synaptic vesicle priming	18	22	3.567e-02
GO:BP	GO:0036480	neuron intrinsic apoptotic signaling pathway in response to oxidative stress	18	22	3.567e-02
GO:BP	GO:1902254	negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator	18	22	3.567e-02
GO:BP	GO:0002089	lens morphogenesis in camera-type eye	18	22	3.567e-02
GO:BP	GO:0046485	ether lipid metabolic process	18	22	3.567e-02
GO:BP	GO:2000001	regulation of DNA damage checkpoint	18	22	3.567e-02
GO:BP	GO:0032012	regulation of ARF protein signal transduction	18	22	3.567e-02
GO:BP	GO:0006662	glycerol ether metabolic process	18	22	3.567e-02
GO:BP	GO:0032011	ARF protein signal transduction	18	22	3.567e-02
GO:BP	GO:0034350	regulation of glial cell apoptotic process	11	12	3.614e-02
GO:BP	GO:0032793	positive regulation of CREB transcription factor activity	11	12	3.614e-02
GO:BP	GO:0006285	base-excision repair, AP site formation	11	12	3.614e-02
GO:BP	GO:0034139	regulation of toll-like receptor 3 signaling pathway	11	12	3.614e-02
GO:BP	GO:0000413	protein peptidyl-prolyl isomerization	22	28	3.614e-02
GO:BP	GO:0034138	toll-like receptor 3 signaling pathway	20	25	3.614e-02
GO:BP	GO:1904867	protein localization to Cajal body	11	12	3.614e-02
GO:BP	GO:0000305	response to oxygen radical	22	28	3.614e-02
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	70	105	3.614e-02
GO:BP	GO:0010661	positive regulation of muscle cell apoptotic process	22	28	3.614e-02
GO:BP	GO:0001783	B cell apoptotic process	20	25	3.614e-02
GO:BP	GO:0032925	regulation of activin receptor signaling pathway	20	25	3.614e-02
GO:BP	GO:0046039	GTP metabolic process	20	25	3.614e-02
GO:BP	GO:0099515	actin filament-based transport	11	12	3.614e-02
GO:BP	GO:0051882	mitochondrial depolarization	20	25	3.614e-02
GO:BP	GO:1903441	protein localization to ciliary membrane	11	12	3.614e-02
GO:BP	GO:1903405	protein localization to nuclear body	11	12	3.614e-02
GO:BP	GO:0044346	fibroblast apoptotic process	20	25	3.614e-02
GO:BP	GO:0060379	cardiac muscle cell myoblast differentiation	11	12	3.614e-02
GO:BP	GO:0060586	multicellular organismal-level iron ion homeostasis	22	28	3.614e-02
GO:BP	GO:0001967	suckling behavior	11	12	3.614e-02
GO:BP	GO:0043403	skeletal muscle tissue regeneration	33	45	3.614e-02
GO:BP	GO:0008611	ether lipid biosynthetic process	11	12	3.614e-02
GO:BP	GO:0071394	cellular response to testosterone stimulus	11	12	3.614e-02
GO:BP	GO:0042939	tripeptide transport	11	12	3.614e-02
GO:BP	GO:0061339	establishment or maintenance of monopolar cell polarity	20	25	3.614e-02
GO:BP	GO:0042364	water-soluble vitamin biosynthetic process	11	12	3.614e-02
GO:BP	GO:1903897	regulation of PERK-mediated unfolded protein response	11	12	3.614e-02
GO:BP	GO:0048755	branching morphogenesis of a nerve	11	12	3.614e-02
GO:BP	GO:0007175	negative regulation of epidermal growth factor-activated receptor activity	11	12	3.614e-02
GO:BP	GO:0048499	synaptic vesicle membrane organization	22	28	3.614e-02
GO:BP	GO:0035335	peptidyl-tyrosine dephosphorylation	20	25	3.614e-02
GO:BP	GO:0003207	cardiac chamber formation	11	12	3.614e-02
GO:BP	GO:0002253	activation of immune response	334	560	3.614e-02
GO:BP	GO:0034975	protein folding in endoplasmic reticulum	11	12	3.614e-02
GO:BP	GO:0033688	regulation of osteoblast proliferation	22	28	3.614e-02
GO:BP	GO:1900152	negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	11	12	3.614e-02
GO:BP	GO:0021544	subpallium development	22	28	3.614e-02
GO:BP	GO:1905671	regulation of lysosome organization	11	12	3.614e-02
GO:BP	GO:0046504	glycerol ether biosynthetic process	11	12	3.614e-02
GO:BP	GO:2000009	negative regulation of protein localization to cell surface	11	12	3.614e-02
GO:BP	GO:0031340	positive regulation of vesicle fusion	11	12	3.614e-02
GO:BP	GO:0031293	membrane protein intracellular domain proteolysis	11	12	3.614e-02
GO:BP	GO:0006312	mitotic recombination	20	25	3.614e-02
GO:BP	GO:0021670	lateral ventricle development	11	12	3.614e-02
GO:BP	GO:2000651	positive regulation of sodium ion transmembrane transporter activity	11	12	3.614e-02
GO:BP	GO:0051386	regulation of neurotrophin TRK receptor signaling pathway	11	12	3.614e-02
GO:BP	GO:0051282	regulation of sequestering of calcium ion	85	130	3.618e-02
GO:BP	GO:0009064	glutamine family amino acid metabolic process	56	82	3.623e-02
GO:BP	GO:0042246	tissue regeneration	56	82	3.623e-02
GO:BP	GO:0061724	lipophagy	8	8	3.639e-02
GO:BP	GO:0062196	regulation of lysosome size	8	8	3.639e-02
GO:BP	GO:0000056	ribosomal small subunit export from nucleus	8	8	3.639e-02
GO:BP	GO:1903943	regulation of hepatocyte apoptotic process	8	8	3.639e-02
GO:BP	GO:0090063	positive regulation of microtubule nucleation	8	8	3.639e-02
GO:BP	GO:0036289	peptidyl-serine autophosphorylation	8	8	3.639e-02
GO:BP	GO:0070127	tRNA aminoacylation for mitochondrial protein translation	8	8	3.639e-02
GO:BP	GO:0046984	regulation of hemoglobin biosynthetic process	8	8	3.639e-02
GO:BP	GO:2000726	negative regulation of cardiac muscle cell differentiation	8	8	3.639e-02
GO:BP	GO:1902913	positive regulation of neuroepithelial cell differentiation	8	8	3.639e-02
GO:BP	GO:0046492	heme B metabolic process	8	8	3.639e-02
GO:BP	GO:0003149	membranous septum morphogenesis	8	8	3.639e-02
GO:BP	GO:0036261	7-methylguanosine cap hypermethylation	8	8	3.639e-02
GO:BP	GO:1903108	regulation of mitochondrial transcription	8	8	3.639e-02
GO:BP	GO:0006551	L-leucine metabolic process	8	8	3.639e-02
GO:BP	GO:0000965	mitochondrial RNA 3’-end processing	8	8	3.639e-02
GO:BP	GO:0106354	tRNA surveillance	8	8	3.639e-02
GO:BP	GO:0060509	type I pneumocyte differentiation	8	8	3.639e-02
GO:BP	GO:1903608	protein localization to cytoplasmic stress granule	8	8	3.639e-02
GO:BP	GO:0060600	dichotomous subdivision of an epithelial terminal unit	8	8	3.639e-02
GO:BP	GO:0043504	mitochondrial DNA repair	8	8	3.639e-02
GO:BP	GO:0061343	cell adhesion involved in heart morphogenesis	8	8	3.639e-02
GO:BP	GO:0051086	chaperone mediated protein folding independent of cofactor	8	8	3.639e-02
GO:BP	GO:0006616	SRP-dependent cotranslational protein targeting to membrane, translocation	8	8	3.639e-02
GO:BP	GO:0120180	cell-substrate junction disassembly	8	8	3.639e-02
GO:BP	GO:1903147	negative regulation of autophagy of mitochondrion	8	8	3.639e-02
GO:BP	GO:0120181	focal adhesion disassembly	8	8	3.639e-02
GO:BP	GO:0006785	heme B biosynthetic process	8	8	3.639e-02
GO:BP	GO:0071051	poly(A)-dependent snoRNA 3’-end processing	8	8	3.639e-02
GO:BP	GO:0060675	ureteric bud morphogenesis	48	69	3.639e-02
GO:BP	GO:0018202	peptidyl-histidine modification	8	8	3.639e-02
GO:BP	GO:0035434	copper ion transmembrane transport	8	8	3.639e-02
GO:BP	GO:0072033	renal vesicle formation	8	8	3.639e-02
GO:BP	GO:1905064	negative regulation of vascular associated smooth muscle cell differentiation	8	8	3.639e-02
GO:BP	GO:0015959	diadenosine polyphosphate metabolic process	8	8	3.639e-02
GO:BP	GO:1901401	regulation of tetrapyrrole metabolic process	8	8	3.639e-02
GO:BP	GO:2000643	positive regulation of early endosome to late endosome transport	8	8	3.639e-02
GO:BP	GO:0006384	transcription initiation at RNA polymerase III promoter	8	8	3.639e-02
GO:BP	GO:2000586	regulation of platelet-derived growth factor receptor-beta signaling pathway	8	8	3.639e-02
GO:BP	GO:0031118	rRNA pseudouridine synthesis	8	8	3.639e-02
GO:BP	GO:1901525	negative regulation of mitophagy	8	8	3.639e-02
GO:BP	GO:0033152	immunoglobulin V(D)J recombination	8	8	3.639e-02
GO:BP	GO:2000601	positive regulation of Arp2/3 complex-mediated actin nucleation	8	8	3.639e-02
GO:BP	GO:0032906	transforming growth factor beta2 production	8	8	3.639e-02
GO:BP	GO:0010793	regulation of mRNA export from nucleus	8	8	3.639e-02
GO:BP	GO:0048227	plasma membrane to endosome transport	8	8	3.639e-02
GO:BP	GO:0032909	regulation of transforming growth factor beta2 production	8	8	3.639e-02
GO:BP	GO:0034775	glutathione transmembrane transport	8	8	3.639e-02
GO:BP	GO:0032347	regulation of aldosterone biosynthetic process	8	8	3.639e-02
GO:BP	GO:0010835	regulation of protein ADP-ribosylation	8	8	3.639e-02
GO:BP	GO:0071499	cellular response to laminar fluid shear stress	8	8	3.639e-02
GO:BP	GO:0034475	U4 snRNA 3’-end processing	8	8	3.639e-02
GO:BP	GO:0150012	positive regulation of neuron projection arborization	8	8	3.639e-02
GO:BP	GO:0003223	ventricular compact myocardium morphogenesis	8	8	3.639e-02
GO:BP	GO:0031077	post-embryonic camera-type eye development	8	8	3.639e-02
GO:BP	GO:0032344	regulation of aldosterone metabolic process	8	8	3.639e-02
GO:BP	GO:1904354	negative regulation of telomere capping	8	8	3.639e-02
GO:BP	GO:0051683	establishment of Golgi localization	8	8	3.639e-02
GO:BP	GO:0017185	peptidyl-lysine hydroxylation	8	8	3.639e-02
GO:BP	GO:0045008	depyrimidination	8	8	3.639e-02
GO:BP	GO:0072330	monocarboxylic acid biosynthetic process	134	213	3.644e-02
GO:BP	GO:0010596	negative regulation of endothelial cell migration	38	53	3.662e-02
GO:BP	GO:0071260	cellular response to mechanical stimulus	51	74	3.768e-02
GO:BP	GO:0036297	interstrand cross-link repair	31	42	3.779e-02
GO:BP	GO:2001251	negative regulation of chromosome organization	65	97	3.833e-02
GO:BP	GO:0061041	regulation of wound healing	86	132	3.892e-02
GO:BP	GO:0060760	positive regulation of response to cytokine stimulus	46	66	3.939e-02
GO:BP	GO:0021795	cerebral cortex cell migration	36	50	4.002e-02
GO:BP	GO:0007019	microtubule depolymerization	36	50	4.002e-02
GO:BP	GO:0000070	mitotic sister chromatid segregation	122	193	4.035e-02
GO:BP	GO:1902107	positive regulation of leukocyte differentiation	122	193	4.035e-02
GO:BP	GO:1903708	positive regulation of hemopoiesis	122	193	4.035e-02
GO:BP	GO:0050685	positive regulation of mRNA processing	29	39	4.059e-02
GO:BP	GO:0044409	symbiont entry into host	93	144	4.157e-02
GO:BP	GO:0046718	symbiont entry into host cell	90	139	4.211e-02
GO:BP	GO:0019217	regulation of fatty acid metabolic process	63	94	4.243e-02
GO:BP	GO:1903725	regulation of phospholipid metabolic process	27	36	4.341e-02
GO:BP	GO:0033144	negative regulation of intracellular steroid hormone receptor signaling pathway	27	36	4.341e-02
GO:BP	GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	27	36	4.341e-02
GO:BP	GO:0009156	ribonucleoside monophosphate biosynthetic process	27	36	4.341e-02
GO:BP	GO:0048332	mesoderm morphogenesis	52	76	4.344e-02
GO:BP	GO:0048709	oligodendrocyte differentiation	72	109	4.349e-02
GO:BP	GO:0008038	neuron recognition	34	47	4.356e-02
GO:BP	GO:0031641	regulation of myelination	34	47	4.356e-02
GO:BP	GO:0045778	positive regulation of ossification	39	55	4.422e-02
GO:BP	GO:0055012	ventricular cardiac muscle cell differentiation	13	15	4.432e-02
GO:BP	GO:0051444	negative regulation of ubiquitin-protein transferase activity	13	15	4.432e-02
GO:BP	GO:0060026	convergent extension	13	15	4.432e-02
GO:BP	GO:0046761	viral budding from plasma membrane	13	15	4.432e-02
GO:BP	GO:0045176	apical protein localization	13	15	4.432e-02
GO:BP	GO:0051284	positive regulation of sequestering of calcium ion	13	15	4.432e-02
GO:BP	GO:0098969	neurotransmitter receptor transport to postsynaptic membrane	13	15	4.432e-02
GO:BP	GO:0006750	glutathione biosynthetic process	13	15	4.432e-02
GO:BP	GO:1903894	regulation of IRE1-mediated unfolded protein response	13	15	4.432e-02
GO:BP	GO:0007176	regulation of epidermal growth factor-activated receptor activity	13	15	4.432e-02
GO:BP	GO:0009209	pyrimidine ribonucleoside triphosphate biosynthetic process	13	15	4.432e-02
GO:BP	GO:1902166	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	13	15	4.432e-02
GO:BP	GO:0010715	regulation of extracellular matrix disassembly	13	15	4.432e-02
GO:BP	GO:0014029	neural crest formation	13	15	4.432e-02
GO:BP	GO:0150011	regulation of neuron projection arborization	13	15	4.432e-02
GO:BP	GO:1903543	positive regulation of exosomal secretion	13	15	4.432e-02
GO:BP	GO:0099118	microtubule-based protein transport	13	15	4.432e-02
GO:BP	GO:0098840	protein transport along microtubule	13	15	4.432e-02
GO:BP	GO:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	13	15	4.432e-02
GO:BP	GO:0097212	lysosomal membrane organization	13	15	4.432e-02
GO:BP	GO:0006474	N-terminal protein amino acid acetylation	13	15	4.432e-02
GO:BP	GO:0090030	regulation of steroid hormone biosynthetic process	13	15	4.432e-02
GO:BP	GO:2001028	positive regulation of endothelial cell chemotaxis	13	15	4.432e-02
GO:BP	GO:0008298	intracellular mRNA localization	13	15	4.432e-02
GO:BP	GO:0006047	UDP-N-acetylglucosamine metabolic process	13	15	4.432e-02
GO:BP	GO:0033146	regulation of intracellular estrogen receptor signaling pathway	25	33	4.568e-02
GO:BP	GO:0033198	response to ATP	25	33	4.568e-02
GO:BP	GO:0033687	osteoblast proliferation	25	33	4.568e-02
GO:BP	GO:0051346	negative regulation of hydrolase activity	58	86	4.568e-02
GO:BP	GO:0018208	peptidyl-proline modification	25	33	4.568e-02
GO:BP	GO:0050806	positive regulation of synaptic transmission	114	180	4.602e-02
GO:BP	GO:0009914	hormone transport	204	335	4.693e-02
GO:BP	GO:0060236	regulation of mitotic spindle organization	32	44	4.697e-02
GO:BP	GO:0048821	erythrocyte development	32	44	4.697e-02
GO:BP	GO:0030501	positive regulation of bone mineralization	32	44	4.697e-02
GO:BP	GO:0030835	negative regulation of actin filament depolymerization	32	44	4.697e-02
GO:BP	GO:0010812	negative regulation of cell-substrate adhesion	42	60	4.735e-02
GO:BP	GO:1904888	cranial skeletal system development	50	73	4.756e-02
GO:BP	GO:0061371	determination of heart left/right asymmetry	50	73	4.756e-02
GO:BP	GO:0003333	amino acid transmembrane transport	70	106	4.762e-02
GO:BP	GO:0044344	cellular response to fibroblast growth factor stimulus	73	111	4.763e-02
GO:BP	GO:0060055	angiogenesis involved in wound healing	23	30	4.786e-02
GO:BP	GO:1903077	negative regulation of protein localization to plasma membrane	23	30	4.786e-02
GO:BP	GO:0048261	negative regulation of receptor-mediated endocytosis	23	30	4.786e-02
GO:BP	GO:0008299	isoprenoid biosynthetic process	23	30	4.786e-02
GO:BP	GO:0051291	protein heterooligomerization	23	30	4.786e-02
GO:BP	GO:0021952	central nervous system projection neuron axonogenesis	23	30	4.786e-02
GO:BP	GO:0071577	zinc ion transmembrane transport	23	30	4.786e-02
GO:BP	GO:0046621	negative regulation of organ growth	23	30	4.786e-02
GO:BP	GO:0098813	nuclear chromosome segregation	197	323	4.786e-02
GO:BP	GO:0045830	positive regulation of isotype switching	23	30	4.786e-02
GO:BP	GO:0006541	glutamine metabolic process	23	30	4.786e-02
GO:BP	GO:0030520	estrogen receptor signaling pathway	37	52	4.786e-02
GO:BP	GO:0006044	N-acetylglucosamine metabolic process	15	18	4.885e-02
GO:BP	GO:0046184	aldehyde biosynthetic process	15	18	4.885e-02
GO:BP	GO:0010002	cardioblast differentiation	15	18	4.885e-02
GO:BP	GO:1905038	regulation of membrane lipid metabolic process	15	18	4.885e-02
GO:BP	GO:0061577	calcium ion transmembrane transport via high voltage-gated calcium channel	15	18	4.885e-02
GO:BP	GO:0055119	relaxation of cardiac muscle	15	18	4.885e-02
GO:BP	GO:0003128	heart field specification	15	18	4.885e-02
GO:BP	GO:1902570	protein localization to nucleolus	15	18	4.885e-02
GO:BP	GO:0000303	response to superoxide	21	27	4.963e-02
GO:BP	GO:1902914	regulation of protein polyubiquitination	21	27	4.963e-02
GO:BP	GO:0021697	cerebellar cortex formation	21	27	4.963e-02
GO:BP	GO:0018904	ether metabolic process	21	27	4.963e-02
GO:BP	GO:0007498	mesoderm development	89	138	4.963e-02
GO:BP	GO:0036344	platelet morphogenesis	21	27	4.963e-02
GO:BP	GO:0006929	substrate-dependent cell migration	21	27	4.963e-02
GO:BP	GO:0043525	positive regulation of neuron apoptotic process	45	65	4.985e-02
GO:BP	GO:0140895	cell surface toll-like receptor signaling pathway	45	65	4.985e-02
GO:BP	GO:0006261	DNA-templated DNA replication	102	160	4.986e-02
KEGG	KEGG:04141	Protein processing in endoplasmic reticulum	161	168	5.294e-20
KEGG	KEGG:04144	Endocytosis	224	248	9.101e-19
KEGG	KEGG:04140	Autophagy - animal	157	165	9.101e-19
KEGG	KEGG:05168	Herpes simplex virus 1 infection	419	506	3.468e-18
KEGG	KEGG:04120	Ubiquitin mediated proteolysis	130	140	3.751e-13
KEGG	KEGG:05014	Amyotrophic lateral sclerosis	300	363	1.152e-12
KEGG	KEGG:05022	Pathways of neurodegeneration - multiple diseases	381	474	1.357e-12
KEGG	KEGG:04137	Mitophagy - animal	98	103	7.432e-12
KEGG	KEGG:05012	Parkinson disease	224	265	1.607e-11
KEGG	KEGG:05010	Alzheimer disease	309	382	6.802e-11
KEGG	KEGG:05016	Huntington disease	252	305	8.998e-11
KEGG	KEGG:05132	Salmonella infection	208	249	9.046e-10
KEGG	KEGG:04360	Axon guidance	156	181	1.913e-09
KEGG	KEGG:04919	Thyroid hormone signaling pathway	109	121	3.660e-09
KEGG	KEGG:05131	Shigellosis	204	246	4.362e-09
KEGG	KEGG:04150	mTOR signaling pathway	135	155	6.227e-09
KEGG	KEGG:04714	Thermogenesis	193	232	6.974e-09
KEGG	KEGG:04722	Neurotrophin signaling pathway	106	118	7.758e-09
KEGG	KEGG:03013	Nucleocytoplasmic transport	98	108	8.565e-09
KEGG	KEGG:04142	Lysosome	116	131	9.088e-09
KEGG	KEGG:05210	Colorectal cancer	80	86	1.467e-08
KEGG	KEGG:04910	Insulin signaling pathway	120	137	2.048e-08
KEGG	KEGG:05017	Spinocerebellar ataxia	123	141	2.189e-08
KEGG	KEGG:03018	RNA degradation	74	79	2.347e-08
KEGG	KEGG:03083	Polycomb repressive complex	78	84	2.558e-08
KEGG	KEGG:05212	Pancreatic cancer	71	76	6.356e-08
KEGG	KEGG:05220	Chronic myeloid leukemia	71	76	6.356e-08
KEGG	KEGG:00970	Aminoacyl-tRNA biosynthesis	44	44	6.730e-08
KEGG	KEGG:01100	Metabolic pathways	1094	1537	7.100e-08
KEGG	KEGG:04012	ErbB signaling pathway	77	84	1.336e-07
KEGG	KEGG:04510	Focal adhesion	167	202	1.538e-07
KEGG	KEGG:04070	Phosphatidylinositol signaling system	87	97	2.067e-07
KEGG	KEGG:05208	Chemical carcinogenesis - reactive oxygen species	180	221	3.718e-07
KEGG	KEGG:04931	Insulin resistance	95	108	4.514e-07
KEGG	KEGG:00510	N-Glycan biosynthesis	51	53	4.721e-07
KEGG	KEGG:01521	EGFR tyrosine kinase inhibitor resistance	72	79	6.376e-07
KEGG	KEGG:05213	Endometrial cancer	55	58	6.377e-07
KEGG	KEGG:05020	Prion disease	215	271	1.009e-06
KEGG	KEGG:05100	Bacterial invasion of epithelial cells	70	77	1.173e-06
KEGG	KEGG:03010	Ribosome	128	153	1.540e-06
KEGG	KEGG:05225	Hepatocellular carcinoma	137	166	2.931e-06
KEGG	KEGG:04932	Non-alcoholic fatty liver disease	128	154	3.142e-06
KEGG	KEGG:03020	RNA polymerase	34	34	3.370e-06
KEGG	KEGG:03015	mRNA surveillance pathway	84	96	3.672e-06
KEGG	KEGG:05415	Diabetic cardiomyopathy	163	202	4.013e-06
KEGG	KEGG:05211	Renal cell carcinoma	62	68	4.140e-06
KEGG	KEGG:05223	Non-small cell lung cancer	65	72	5.340e-06
KEGG	KEGG:04520	Adherens junction	81	93	8.394e-06
KEGG	KEGG:04933	AGE-RAGE signaling pathway in diabetic complications	86	100	1.277e-05
KEGG	KEGG:04071	Sphingolipid signaling pathway	101	120	1.379e-05
KEGG	KEGG:04152	AMPK signaling pathway	101	120	1.379e-05
KEGG	KEGG:00310	Lysine degradation	57	63	2.034e-05
KEGG	KEGG:05165	Human papillomavirus infection	252	330	2.213e-05
KEGG	KEGG:04010	MAPK signaling pathway	231	301	2.948e-05
KEGG	KEGG:03082	ATP-dependent chromatin remodeling	97	116	3.707e-05
KEGG	KEGG:04390	Hippo signaling pathway	127	157	4.644e-05
KEGG	KEGG:01200	Carbon metabolism	96	115	4.649e-05
KEGG	KEGG:04211	Longevity regulating pathway	76	89	7.703e-05
KEGG	KEGG:05222	Small cell lung cancer	78	92	1.024e-04
KEGG	KEGG:04136	Autophagy - other	31	32	1.057e-04
KEGG	KEGG:03022	Basal transcription factors	40	43	1.086e-04
KEGG	KEGG:01212	Fatty acid metabolism	51	57	1.267e-04
KEGG	KEGG:04218	Cellular senescence	124	155	1.484e-04
KEGG	KEGG:03060	Protein export	30	31	1.484e-04
KEGG	KEGG:05231	Choline metabolism in cancer	82	98	1.592e-04
KEGG	KEGG:00562	Inositol phosphate metabolism	63	73	1.882e-04
KEGG	KEGG:04210	Apoptosis	109	135	1.985e-04
KEGG	KEGG:03050	Proteasome	42	46	1.985e-04
KEGG	KEGG:04310	Wnt signaling pathway	137	174	2.346e-04
KEGG	KEGG:05205	Proteoglycans in cancer	159	205	2.614e-04
KEGG	KEGG:04146	Peroxisome	70	83	3.332e-04
KEGG	KEGG:00520	Amino sugar and nucleotide sugar metabolism	44	49	3.363e-04
KEGG	KEGG:05135	Yersinia infection	109	136	3.382e-04
KEGG	KEGG:03250	Viral life cycle - HIV-1	54	62	3.571e-04
KEGG	KEGG:04261	Adrenergic signaling in cardiomyocytes	121	153	4.151e-04
KEGG	KEGG:04810	Regulation of actin cytoskeleton	173	227	6.456e-04
KEGG	KEGG:04350	TGF-beta signaling pathway	87	107	6.569e-04
KEGG	KEGG:00513	Various types of N-glycan biosynthesis	38	42	6.857e-04
KEGG	KEGG:01250	Biosynthesis of nucleotide sugars	34	37	7.303e-04
KEGG	KEGG:01522	Endocrine resistance	78	95	7.466e-04
KEGG	KEGG:05214	Glioma	63	75	8.654e-04
KEGG	KEGG:00190	Oxidative phosphorylation	106	134	1.011e-03
KEGG	KEGG:00020	Citrate cycle (TCA cycle)	28	30	1.434e-03
KEGG	KEGG:04213	Longevity regulating pathway - multiple species	52	61	1.434e-03
KEGG	KEGG:00280	Valine, leucine and isoleucine degradation	42	48	1.635e-03
KEGG	KEGG:04340	Hedgehog signaling pathway	48	56	1.818e-03
KEGG	KEGG:04710	Circadian rhythm	31	34	1.904e-03
KEGG	KEGG:05161	Hepatitis B	125	162	1.909e-03
KEGG	KEGG:05200	Pathways in cancer	377	527	2.096e-03
KEGG	KEGG:05215	Prostate cancer	78	97	2.415e-03
KEGG	KEGG:04148	Efferocytosis	120	156	2.935e-03
KEGG	KEGG:05110	Vibrio cholerae infection	43	50	2.935e-03
KEGG	KEGG:05216	Thyroid cancer	33	37	3.057e-03
KEGG	KEGG:05418	Fluid shear stress and atherosclerosis	107	138	3.284e-03
KEGG	KEGG:04130	SNARE interactions in vesicular transport	29	32	3.480e-03
KEGG	KEGG:00900	Terpenoid backbone biosynthesis	21	22	3.547e-03
KEGG	KEGG:05203	Viral carcinogenesis	151	201	4.068e-03
KEGG	KEGG:04530	Tight junction	129	170	4.652e-03
KEGG	KEGG:04330	Notch signaling pathway	50	60	4.734e-03
KEGG	KEGG:00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis	24	26	5.153e-03
KEGG	KEGG:04728	Dopaminergic synapse	101	131	5.952e-03
KEGG	KEGG:04370	VEGF signaling pathway	49	59	5.965e-03
KEGG	KEGG:05120	Epithelial cell signaling in Helicobacter pylori infection	57	70	6.420e-03
KEGG	KEGG:05230	Central carbon metabolism in cancer	57	70	6.420e-03
KEGG	KEGG:04022	cGMP-PKG signaling pathway	124	164	6.758e-03
KEGG	KEGG:04015	Rap1 signaling pathway	156	210	7.104e-03
KEGG	KEGG:03420	Nucleotide excision repair	50	61	8.999e-03
KEGG	KEGG:04068	FoxO signaling pathway	100	131	1.024e-02
KEGG	KEGG:04922	Glucagon signaling pathway	83	107	1.024e-02
KEGG	KEGG:05163	Human cytomegalovirus infection	164	223	1.097e-02
KEGG	KEGG:04666	Fc gamma R-mediated phagocytosis	75	96	1.118e-02
KEGG	KEGG:04720	Long-term potentiation	54	67	1.210e-02
KEGG	KEGG:00062	Fatty acid elongation	24	27	1.550e-02
KEGG	KEGG:01040	Biosynthesis of unsaturated fatty acids	24	27	1.550e-02
KEGG	KEGG:05170	Human immunodeficiency virus 1 infection	154	210	1.652e-02
KEGG	KEGG:05410	Hypertrophic cardiomyopathy	75	97	1.735e-02
KEGG	KEGG:01524	Platinum drug resistance	57	72	1.894e-02
KEGG	KEGG:04912	GnRH signaling pathway	72	93	1.894e-02
KEGG	KEGG:04935	Growth hormone synthesis, secretion and action	91	120	1.961e-02
KEGG	KEGG:05235	PD-L1 expression and PD-1 checkpoint pathway in cancer	69	89	2.068e-02
KEGG	KEGG:04066	HIF-1 signaling pathway	83	109	2.250e-02
KEGG	KEGG:04926	Relaxin signaling pathway	97	129	2.271e-02
KEGG	KEGG:05221	Acute myeloid leukemia	53	67	2.410e-02
KEGG	KEGG:04928	Parathyroid hormone synthesis, secretion and action	80	105	2.410e-02
KEGG	KEGG:00532	Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate	19	21	2.410e-02
KEGG	KEGG:04540	Gap junction	68	88	2.410e-02
KEGG	KEGG:03040	Spliceosome	128	174	2.492e-02
KEGG	KEGG:04917	Prolactin signaling pathway	55	70	2.631e-02
KEGG	KEGG:04920	Adipocytokine signaling pathway	55	70	2.631e-02
KEGG	KEGG:04392	Hippo signaling pathway - multiple species	25	29	2.691e-02
KEGG	KEGG:01210	2-Oxocarboxylic acid metabolism	28	33	2.691e-02
KEGG	KEGG:04962	Vasopressin-regulated water reabsorption	36	44	3.040e-02
KEGG	KEGG:04668	TNF signaling pathway	85	113	3.240e-02
KEGG	KEGG:05130	Pathogenic Escherichia coli infection	143	197	3.381e-02
KEGG	KEGG:04215	Apoptosis - multiple species	27	32	3.462e-02
KEGG	KEGG:05226	Gastric cancer	109	148	3.720e-02
KEGG	KEGG:05414	Dilated cardiomyopathy	77	102	3.720e-02
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	157	218	3.789e-02
KEGG	KEGG:04371	Apelin signaling pathway	102	138	3.789e-02
KEGG	KEGG:00785	Lipoic acid metabolism	17	19	4.240e-02
KEGG	KEGG:01230	Biosynthesis of amino acids	57	74	4.318e-02

# write.csv(table_motif1_GOKEGG_genes, "data/new/table_motif1_GOKEGG_genes.csv")

#GO:BP
table_motif1_genes_GOBP_RUV_clust <- table_motif1_GOKEGG_genes_RUV_clust %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif1_genes_GOBP, "data/table_motif1_genes_GOBP.RDS")

table_motif1_genes_GOBP_RUV_clust %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M1 Enriched GO:BP Terms RUVs clustlike")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG Cormotif log2cpm clustlike only-2.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#KEGG
table_motif1_genes_KEGG_RUV_clust <- table_motif1_GOKEGG_genes_RUV_clust %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif1_genes_KEGG_RUV_clust %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M1 DEGs Enriched KEGG Terms RUVs clustlike")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG Cormotif log2cpm clustlike only-3.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#####Motif 2 Genes#####
# motif2_genes_matrix_RUV_clust <- as.matrix(clust2_genes_RUV)
# colnames(motif2_genes_matrix_RUV_clust) <- c("entrezgene_ID")

# saveRDS(motif2_genes_matrix_RUV_clust, "data/new/RUV/CMF/motif2_genes_matrix_RUV_clustlike.RDS")

motif2_genes_matrix_RUV_clust <- readRDS("data/new/RUV/CMF/motif2_genes_matrix_RUV_clustlike.RDS")
length(motif2_genes_matrix_RUV_clust)

[1] 517

#517 genes in this set for motif 2

motif2_mat_GOKEGG_RUV_clust <- gost(query = motif2_genes_matrix_RUV_clust,
                          organism = "hsapiens",
                          ordered_query = FALSE,
                          measure_underrepresentation = FALSE,
                          evcodes = FALSE,
                          user_threshold = 0.05,
                          correction_method = c("fdr"),
                          sources = c("GO:BP", "KEGG"))

motif2_GOKEGG_genes_RUV_clust <- gostplot(motif2_mat_GOKEGG_RUV_clust, capped = FALSE, interactive = TRUE)
motif2_GOKEGG_genes_RUV_clust

table_motif2_GOKEGG_genes_RUV_clust <- motif2_mat_GOKEGG_RUV_clust$result %>% 
  dplyr::select(c(source, term_id, term_name, intersection_size, term_size, p_value))

table_motif2_GOKEGG_genes_RUV_clust %>% 
  mutate_at(.vars = 6, .funs = scales::label_scientific(digits=4)) %>% 
  kableExtra::kable(.,) %>% 
  kableExtra::kable_paper("striped", full_width = FALSE) %>% 
  kableExtra::kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "hover")) %>% 
  kableExtra::scroll_box(width = "100%", height = "400px")

source	term_id	term_name	intersection_size	term_size	p_value
GO:BP	GO:0022402	cell cycle process	176	1280	7.756e-89
GO:BP	GO:1903047	mitotic cell cycle process	135	745	2.136e-81
GO:BP	GO:0007049	cell cycle	186	1663	1.521e-79
GO:BP	GO:0000278	mitotic cell cycle	142	892	1.736e-78
GO:BP	GO:0007059	chromosome segregation	97	427	1.412e-66
GO:BP	GO:0000280	nuclear division	95	452	7.896e-62
GO:BP	GO:0051301	cell division	109	658	1.822e-60
GO:BP	GO:0010564	regulation of cell cycle process	112	720	2.287e-59
GO:BP	GO:0048285	organelle fission	96	500	7.533e-59
GO:BP	GO:0098813	nuclear chromosome segregation	80	323	1.398e-57
GO:BP	GO:0140014	mitotic nuclear division	73	282	8.759e-54
GO:BP	GO:0051726	regulation of cell cycle	127	1087	1.616e-53
GO:BP	GO:0051276	chromosome organization	95	574	3.075e-52
GO:BP	GO:0000070	mitotic sister chromatid segregation	62	193	8.516e-52
GO:BP	GO:0000819	sister chromatid segregation	66	234	3.728e-51
GO:BP	GO:0044770	cell cycle phase transition	90	532	3.412e-50
GO:BP	GO:0044772	mitotic cell cycle phase transition	79	428	1.318e-46
GO:BP	GO:1901987	regulation of cell cycle phase transition	76	427	1.517e-43
GO:BP	GO:0007346	regulation of mitotic cell cycle	79	492	6.046e-42
GO:BP	GO:0006260	DNA replication	63	283	6.634e-42
GO:BP	GO:0010948	negative regulation of cell cycle process	60	289	6.002e-38
GO:BP	GO:1901990	regulation of mitotic cell cycle phase transition	63	327	6.715e-38
GO:BP	GO:0000075	cell cycle checkpoint signaling	50	185	2.206e-37
GO:BP	GO:1901988	negative regulation of cell cycle phase transition	55	248	2.667e-36
GO:BP	GO:0051983	regulation of chromosome segregation	43	132	7.569e-36
GO:BP	GO:0006261	DNA-templated DNA replication	46	160	1.146e-35
GO:BP	GO:0045786	negative regulation of cell cycle	64	377	3.904e-35
GO:BP	GO:1905818	regulation of chromosome separation	35	77	4.509e-35
GO:BP	GO:0006259	DNA metabolic process	98	1005	1.276e-33
GO:BP	GO:0007088	regulation of mitotic nuclear division	40	121	1.279e-33
GO:BP	GO:0051304	chromosome separation	35	84	1.859e-33
GO:BP	GO:0007093	mitotic cell cycle checkpoint signaling	41	136	1.156e-32
GO:BP	GO:0051310	metaphase chromosome alignment	37	104	2.056e-32
GO:BP	GO:0051783	regulation of nuclear division	42	149	3.681e-32
GO:BP	GO:0090068	positive regulation of cell cycle process	52	262	8.072e-32
GO:BP	GO:1902850	microtubule cytoskeleton organization involved in mitosis	43	169	6.576e-31
GO:BP	GO:1901991	negative regulation of mitotic cell cycle phase transition	43	172	1.435e-30
GO:BP	GO:0050000	chromosome localization	38	126	2.887e-30
GO:BP	GO:0051303	establishment of chromosome localization	37	118	3.735e-30
GO:BP	GO:0045930	negative regulation of mitotic cell cycle	47	225	9.682e-30
GO:BP	GO:0010965	regulation of mitotic sister chromatid separation	29	62	1.724e-29
GO:BP	GO:0007051	spindle organization	45	206	2.435e-29
GO:BP	GO:0051321	meiotic cell cycle	52	297	4.361e-29
GO:BP	GO:0051306	mitotic sister chromatid separation	29	65	9.234e-29
GO:BP	GO:0045787	positive regulation of cell cycle	55	351	2.687e-28
GO:BP	GO:0033045	regulation of sister chromatid segregation	34	107	6.417e-28
GO:BP	GO:0033048	negative regulation of mitotic sister chromatid segregation	26	51	1.024e-27
GO:BP	GO:0045841	negative regulation of mitotic metaphase/anaphase transition	26	51	1.024e-27
GO:BP	GO:1903046	meiotic cell cycle process	45	224	1.024e-27
GO:BP	GO:0033046	negative regulation of sister chromatid segregation	26	51	1.024e-27
GO:BP	GO:2000816	negative regulation of mitotic sister chromatid separation	26	51	1.024e-27
GO:BP	GO:0033047	regulation of mitotic sister chromatid segregation	27	57	1.094e-27
GO:BP	GO:0051784	negative regulation of nuclear division	28	65	2.769e-27
GO:BP	GO:0051985	negative regulation of chromosome segregation	26	53	3.451e-27
GO:BP	GO:1905819	negative regulation of chromosome separation	26	53	3.451e-27
GO:BP	GO:0045839	negative regulation of mitotic nuclear division	27	59	3.451e-27
GO:BP	GO:1902100	negative regulation of metaphase/anaphase transition of cell cycle	26	53	3.451e-27
GO:BP	GO:0006974	DNA damage response	84	908	4.955e-27
GO:BP	GO:0007091	metaphase/anaphase transition of mitotic cell cycle	32	97	6.340e-27
GO:BP	GO:0007052	mitotic spindle organization	36	134	7.920e-27
GO:BP	GO:0007094	mitotic spindle assembly checkpoint signaling	25	49	1.009e-26
GO:BP	GO:0071174	mitotic spindle checkpoint signaling	25	49	1.009e-26
GO:BP	GO:0071173	spindle assembly checkpoint signaling	25	49	1.009e-26
GO:BP	GO:0006281	DNA repair	69	621	1.336e-26
GO:BP	GO:0044784	metaphase/anaphase transition of cell cycle	32	100	1.745e-26
GO:BP	GO:0031577	spindle checkpoint signaling	25	50	1.887e-26
GO:BP	GO:0030071	regulation of mitotic metaphase/anaphase transition	31	93	2.835e-26
GO:BP	GO:0006996	organelle organization	180	3594	3.186e-26
GO:BP	GO:1902099	regulation of metaphase/anaphase transition of cell cycle	31	96	8.462e-26
GO:BP	GO:0140013	meiotic nuclear division	41	202	1.633e-25
GO:BP	GO:0008608	attachment of spindle microtubules to kinetochore	25	54	2.149e-25
GO:BP	GO:0033044	regulation of chromosome organization	43	242	2.480e-24
GO:BP	GO:0000226	microtubule cytoskeleton organization	68	670	6.406e-24
GO:BP	GO:0044839	cell cycle G2/M phase transition	34	156	4.003e-22
GO:BP	GO:0000086	G2/M transition of mitotic cell cycle	32	139	1.407e-21
GO:BP	GO:0007017	microtubule-based process	79	999	5.216e-21
GO:BP	GO:2001251	negative regulation of chromosome organization	27	97	1.692e-20
GO:BP	GO:0006270	DNA replication initiation	19	37	2.581e-20
GO:BP	GO:0051225	spindle assembly	29	136	1.588e-18
GO:BP	GO:0010389	regulation of G2/M transition of mitotic cell cycle	26	105	2.571e-18
GO:BP	GO:0051656	establishment of organelle localization	51	491	4.099e-18
GO:BP	GO:0061982	meiosis I cell cycle process	29	141	4.444e-18
GO:BP	GO:0033554	cellular response to stress	105	1830	9.131e-18
GO:BP	GO:0007080	mitotic metaphase chromosome alignment	21	63	1.064e-17
GO:BP	GO:0033043	regulation of organelle organization	79	1148	2.239e-17
GO:BP	GO:0051640	organelle localization	56	620	3.748e-17
GO:BP	GO:0045132	meiotic chromosome segregation	24	96	5.189e-17
GO:BP	GO:1902749	regulation of cell cycle G2/M phase transition	26	118	5.557e-17
GO:BP	GO:0006302	double-strand break repair	40	319	5.879e-17
GO:BP	GO:1905820	positive regulation of chromosome separation	16	32	7.715e-17
GO:BP	GO:0006310	DNA recombination	41	347	1.850e-16
GO:BP	GO:0000725	recombinational repair	31	193	3.945e-16
GO:BP	GO:0051984	positive regulation of chromosome segregation	15	30	9.009e-16
GO:BP	GO:0000724	double-strand break repair via homologous recombination	30	188	1.600e-15
GO:BP	GO:0044786	cell cycle DNA replication	17	45	2.278e-15
GO:BP	GO:0007010	cytoskeleton organization	89	1529	3.536e-15
GO:BP	GO:0033260	nuclear DNA replication	16	41	1.019e-14
GO:BP	GO:0140694	membraneless organelle assembly	43	430	1.271e-14
GO:BP	GO:0007127	meiosis I	25	133	1.282e-14
GO:BP	GO:0051716	cellular response to stimulus	252	7376	1.396e-14
GO:BP	GO:0051988	regulation of attachment of spindle microtubules to kinetochore	13	23	1.414e-14
GO:BP	GO:0034508	centromere complex assembly	14	29	1.878e-14
GO:BP	GO:0031570	DNA integrity checkpoint signaling	24	123	2.009e-14
GO:BP	GO:1901989	positive regulation of cell cycle phase transition	23	114	3.794e-14
GO:BP	GO:1901992	positive regulation of mitotic cell cycle phase transition	21	93	6.107e-14
GO:BP	GO:0022414	reproductive process	89	1608	6.854e-14
GO:BP	GO:0000727	double-strand break repair via break-induced replication	10	12	8.495e-14
GO:BP	GO:0019953	sexual reproduction	71	1122	1.113e-13
GO:BP	GO:0006275	regulation of DNA replication	23	120	1.181e-13
GO:BP	GO:0051383	kinetochore organization	12	21	1.550e-13
GO:BP	GO:0090329	regulation of DNA-templated DNA replication	15	40	1.592e-13
GO:BP	GO:0035556	intracellular signal transduction	131	2965	2.346e-13
GO:BP	GO:0045931	positive regulation of mitotic cell cycle	23	124	2.408e-13
GO:BP	GO:0010639	negative regulation of organelle organization	36	352	1.628e-12
GO:BP	GO:0051315	attachment of mitotic spindle microtubules to kinetochore	12	25	2.417e-12
GO:BP	GO:0090307	mitotic spindle assembly	18	76	2.471e-12
GO:BP	GO:0030174	regulation of DNA-templated DNA replication initiation	10	15	3.298e-12
GO:BP	GO:0044771	meiotic cell cycle phase transition	10	15	3.298e-12
GO:BP	GO:1901976	regulation of cell cycle checkpoint	15	48	3.420e-12
GO:BP	GO:0050896	response to stimulus	281	8999	8.591e-12
GO:BP	GO:0000910	cytokinesis	26	192	9.081e-12
GO:BP	GO:0000281	mitotic cytokinesis	19	95	1.260e-11
GO:BP	GO:0051128	regulation of cellular component organization	110	2433	1.573e-11
GO:BP	GO:1902969	mitotic DNA replication	10	17	1.952e-11
GO:BP	GO:0051052	regulation of DNA metabolic process	41	500	3.991e-11
GO:BP	GO:0090231	regulation of spindle checkpoint	11	25	8.420e-11
GO:BP	GO:0051231	spindle elongation	9	14	9.241e-11
GO:BP	GO:0032465	regulation of cytokinesis	18	94	1.108e-10
GO:BP	GO:0007143	female meiotic nuclear division	13	42	1.671e-10
GO:BP	GO:0007098	centrosome cycle	21	140	2.373e-10
GO:BP	GO:1901970	positive regulation of mitotic sister chromatid separation	10	21	3.090e-10
GO:BP	GO:0051256	mitotic spindle midzone assembly	8	11	3.443e-10
GO:BP	GO:0000077	DNA damage checkpoint signaling	19	114	3.501e-10
GO:BP	GO:0030261	chromosome condensation	13	45	4.328e-10
GO:BP	GO:0016043	cellular component organization	256	8184	4.428e-10
GO:BP	GO:0000022	mitotic spindle elongation	8	12	9.828e-10
GO:BP	GO:0008283	cell population proliferation	92	2015	1.151e-09
GO:BP	GO:0000082	G1/S transition of mitotic cell cycle	24	202	1.151e-09
GO:BP	GO:0031023	microtubule organizing center organization	21	153	1.258e-09
GO:BP	GO:1903504	regulation of mitotic spindle checkpoint	10	24	1.502e-09
GO:BP	GO:0090266	regulation of mitotic cell cycle spindle assembly checkpoint	10	24	1.502e-09
GO:BP	GO:0061640	cytoskeleton-dependent cytokinesis	19	124	1.507e-09
GO:BP	GO:0051302	regulation of cell division	23	188	1.563e-09
GO:BP	GO:0034502	protein localization to chromosome	19	126	1.980e-09
GO:BP	GO:0071459	protein localization to chromosome, centromeric region	12	41	2.098e-09
GO:BP	GO:0050789	regulation of biological process	345	12336	2.235e-09
GO:BP	GO:0044774	mitotic DNA integrity checkpoint signaling	15	74	2.700e-09
GO:BP	GO:0044843	cell cycle G1/S phase transition	25	230	2.898e-09
GO:BP	GO:0051255	spindle midzone assembly	8	14	5.230e-09
GO:BP	GO:0065004	protein-DNA complex assembly	25	241	7.797e-09
GO:BP	GO:0071840	cellular component organization or biogenesis	256	8393	7.936e-09
GO:BP	GO:0071824	protein-DNA complex organization	26	262	8.902e-09
GO:BP	GO:0034080	CENP-A containing chromatin assembly	7	10	9.668e-09
GO:BP	GO:0031055	chromatin remodeling at centromere	7	10	9.668e-09
GO:BP	GO:0007062	sister chromatid cohesion	13	57	9.808e-09
GO:BP	GO:0006271	DNA strand elongation involved in DNA replication	8	15	1.036e-08
GO:BP	GO:1903083	protein localization to condensed chromosome	8	15	1.036e-08
GO:BP	GO:0034501	protein localization to kinetochore	8	15	1.036e-08
GO:BP	GO:0010972	negative regulation of G2/M transition of mitotic cell cycle	14	69	1.053e-08
GO:BP	GO:0042770	signal transduction in response to DNA damage	21	173	1.132e-08
GO:BP	GO:1902750	negative regulation of cell cycle G2/M phase transition	14	71	1.554e-08
GO:BP	GO:0050794	regulation of cellular process	333	11946	2.253e-08
GO:BP	GO:0006468	protein phosphorylation	63	1227	2.323e-08
GO:BP	GO:0032467	positive regulation of cytokinesis	12	50	2.372e-08
GO:BP	GO:0008315	G2/MI transition of meiotic cell cycle	6	7	2.460e-08
GO:BP	GO:0051338	regulation of transferase activity	36	498	2.516e-08
GO:BP	GO:0016310	phosphorylation	66	1320	2.528e-08
GO:BP	GO:0048522	positive regulation of cellular process	194	5920	2.881e-08
GO:BP	GO:0051382	kinetochore assembly	8	17	3.516e-08
GO:BP	GO:0070925	organelle assembly	56	1046	4.870e-08
GO:BP	GO:1901993	regulation of meiotic cell cycle phase transition	7	12	5.525e-08
GO:BP	GO:0065007	biological regulation	348	12743	5.906e-08
GO:BP	GO:0044818	mitotic G2/M transition checkpoint	12	55	7.338e-08
GO:BP	GO:0051653	spindle localization	13	68	8.832e-08
GO:BP	GO:0051445	regulation of meiotic cell cycle	13	68	8.832e-08
GO:BP	GO:0035825	homologous recombination	13	68	8.832e-08
GO:BP	GO:1905821	positive regulation of chromosome condensation	6	8	8.997e-08
GO:BP	GO:0007076	mitotic chromosome condensation	8	19	9.976e-08
GO:BP	GO:0090232	positive regulation of spindle checkpoint	7	13	1.121e-07
GO:BP	GO:0044773	mitotic DNA damage checkpoint signaling	13	70	1.254e-07
GO:BP	GO:0045005	DNA-templated DNA replication maintenance of fidelity	12	59	1.649e-07
GO:BP	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	9	28	1.680e-07
GO:BP	GO:0010638	positive regulation of organelle organization	34	492	2.119e-07
GO:BP	GO:0051293	establishment of spindle localization	12	63	3.564e-07
GO:BP	GO:0000212	meiotic spindle organization	8	22	3.826e-07
GO:BP	GO:0090306	meiotic spindle assembly	7	15	3.892e-07
GO:BP	GO:1902751	positive regulation of cell cycle G2/M phase transition	9	31	4.493e-07
GO:BP	GO:0006950	response to stress	138	3948	5.713e-07
GO:BP	GO:0048518	positive regulation of biological process	197	6264	5.937e-07
GO:BP	GO:0050790	regulation of catalytic activity	49	928	7.588e-07
GO:BP	GO:2000241	regulation of reproductive process	20	203	9.242e-07
GO:BP	GO:0051781	positive regulation of cell division	14	98	1.014e-06
GO:BP	GO:0071897	DNA biosynthetic process	18	172	1.740e-06
GO:BP	GO:0051447	negative regulation of meiotic cell cycle	7	18	1.740e-06
GO:BP	GO:0009314	response to radiation	30	437	1.772e-06
GO:BP	GO:0051294	establishment of spindle orientation	10	47	1.793e-06
GO:BP	GO:0051129	negative regulation of cellular component organization	40	701	1.937e-06
GO:BP	GO:0007095	mitotic G2 DNA damage checkpoint signaling	9	37	2.322e-06
GO:BP	GO:2001252	positive regulation of chromosome organization	14	105	2.382e-06
GO:BP	GO:0060623	regulation of chromosome condensation	6	12	2.409e-06
GO:BP	GO:0007056	spindle assembly involved in female meiosis	6	12	2.409e-06
GO:BP	GO:0090267	positive regulation of mitotic cell cycle spindle assembly checkpoint	6	12	2.409e-06
GO:BP	GO:1901978	positive regulation of cell cycle checkpoint	7	19	2.582e-06
GO:BP	GO:0048856	anatomical structure development	187	5997	3.371e-06
GO:BP	GO:0000076	DNA replication checkpoint signaling	7	20	3.857e-06
GO:BP	GO:0031297	replication fork processing	10	51	3.883e-06
GO:BP	GO:1903490	positive regulation of mitotic cytokinesis	6	13	4.262e-06
GO:BP	GO:0007144	female meiosis I	6	13	4.262e-06
GO:BP	GO:0032502	developmental process	200	6553	4.478e-06
GO:BP	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity	12	80	4.985e-06
GO:BP	GO:0070192	chromosome organization involved in meiotic cell cycle	11	66	5.266e-06
GO:BP	GO:0007057	spindle assembly involved in female meiosis I	4	4	5.589e-06
GO:BP	GO:0007275	multicellular organism development	154	4727	5.812e-06
GO:BP	GO:0045143	homologous chromosome segregation	11	67	6.087e-06
GO:BP	GO:0046385	deoxyribose phosphate biosynthetic process	6	14	6.980e-06
GO:BP	GO:0090235	regulation of metaphase plate congression	6	14	6.980e-06
GO:BP	GO:0009263	deoxyribonucleotide biosynthetic process	6	14	6.980e-06
GO:BP	GO:0009265	2’-deoxyribonucleotide biosynthetic process	6	14	6.980e-06
GO:BP	GO:0040001	establishment of mitotic spindle localization	9	43	8.440e-06
GO:BP	GO:0007292	female gamete generation	17	174	9.462e-06
GO:BP	GO:0042127	regulation of cell population proliferation	70	1685	9.462e-06
GO:BP	GO:0000731	DNA synthesis involved in DNA repair	9	44	1.026e-05
GO:BP	GO:0051053	negative regulation of DNA metabolic process	15	139	1.249e-05
GO:BP	GO:1902423	regulation of attachment of mitotic spindle microtubules to kinetochore	5	9	1.376e-05
GO:BP	GO:0048519	negative regulation of biological process	180	5834	1.376e-05
GO:BP	GO:0007154	cell communication	197	6540	1.550e-05
GO:BP	GO:2000242	negative regulation of reproductive process	11	74	1.620e-05
GO:BP	GO:0007131	reciprocal meiotic recombination	10	60	1.712e-05
GO:BP	GO:0140527	reciprocal homologous recombination	10	60	1.712e-05
GO:BP	GO:1902412	regulation of mitotic cytokinesis	6	16	1.712e-05
GO:BP	GO:0045840	positive regulation of mitotic nuclear division	9	47	1.785e-05
GO:BP	GO:0090224	regulation of spindle organization	9	48	2.144e-05
GO:BP	GO:0007165	signal transduction	183	6002	2.303e-05
GO:BP	GO:0065009	regulation of molecular function	63	1496	2.309e-05
GO:BP	GO:1902315	nuclear cell cycle DNA replication initiation	4	5	2.445e-05
GO:BP	GO:1902975	mitotic DNA replication initiation	4	5	2.445e-05
GO:BP	GO:1902292	cell cycle DNA replication initiation	4	5	2.445e-05
GO:BP	GO:0110030	regulation of G2/MI transition of meiotic cell cycle	4	5	2.445e-05
GO:BP	GO:0045842	positive regulation of mitotic metaphase/anaphase transition	6	17	2.477e-05
GO:BP	GO:0051307	meiotic chromosome separation	5	10	2.522e-05
GO:BP	GO:0045835	negative regulation of meiotic nuclear division	5	10	2.522e-05
GO:BP	GO:0051649	establishment of localization in cell	78	2010	2.554e-05
GO:BP	GO:0022616	DNA strand elongation	8	37	2.613e-05
GO:BP	GO:0023052	signaling	195	6515	2.782e-05
GO:BP	GO:0051785	positive regulation of nuclear division	10	64	2.979e-05
GO:BP	GO:2000045	regulation of G1/S transition of mitotic cell cycle	15	150	3.003e-05
GO:BP	GO:0045859	regulation of protein kinase activity	26	402	3.204e-05
GO:BP	GO:1902101	positive regulation of metaphase/anaphase transition of cell cycle	6	18	3.513e-05
GO:BP	GO:0043549	regulation of kinase activity	27	431	3.685e-05
GO:BP	GO:0051987	positive regulation of attachment of spindle microtubules to kinetochore	5	11	4.375e-05
GO:BP	GO:1902806	regulation of cell cycle G1/S phase transition	16	176	4.712e-05
GO:BP	GO:0008284	positive regulation of cell population proliferation	45	954	4.781e-05
GO:BP	GO:0071900	regulation of protein serine/threonine kinase activity	19	242	4.995e-05
GO:BP	GO:0048523	negative regulation of cellular process	172	5629	5.020e-05
GO:BP	GO:0032886	regulation of microtubule-based process	20	266	5.281e-05
GO:BP	GO:0006796	phosphate-containing compound metabolic process	88	2407	5.348e-05
GO:BP	GO:0006793	phosphorus metabolic process	88	2410	5.603e-05
GO:BP	GO:0006338	chromatin remodeling	37	725	6.529e-05
GO:BP	GO:0010032	meiotic chromosome condensation	4	6	6.619e-05
GO:BP	GO:1904666	regulation of ubiquitin protein ligase activity	6	20	6.732e-05
GO:BP	GO:0010212	response to ionizing radiation	14	141	6.839e-05
GO:BP	GO:0071478	cellular response to radiation	16	182	6.987e-05
GO:BP	GO:0051347	positive regulation of transferase activity	21	296	7.260e-05
GO:BP	GO:0007064	mitotic sister chromatid cohesion	7	31	8.195e-05
GO:BP	GO:0070507	regulation of microtubule cytoskeleton organization	15	164	8.498e-05
GO:BP	GO:0051130	positive regulation of cellular component organization	49	1105	8.854e-05
GO:BP	GO:0060236	regulation of mitotic spindle organization	8	44	9.506e-05
GO:BP	GO:0051298	centrosome duplication	10	74	1.056e-04
GO:BP	GO:0007276	gamete generation	40	841	1.361e-04
GO:BP	GO:0009792	embryo development ending in birth or egg hatching	35	692	1.396e-04
GO:BP	GO:0048731	system development	130	4053	1.420e-04
GO:BP	GO:1901994	negative regulation of meiotic cell cycle phase transition	4	7	1.439e-04
GO:BP	GO:0044785	metaphase/anaphase transition of meiotic cell cycle	4	7	1.439e-04
GO:BP	GO:0048609	multicellular organismal reproductive process	45	1000	1.478e-04
GO:BP	GO:0001833	inner cell mass cell proliferation	5	14	1.629e-04
GO:BP	GO:0040020	regulation of meiotic nuclear division	7	35	1.848e-04
GO:BP	GO:0006325	chromatin organization	41	884	1.848e-04
GO:BP	GO:0033316	meiotic spindle assembly checkpoint signaling	3	3	1.889e-04
GO:BP	GO:0110032	positive regulation of G2/MI transition of meiotic cell cycle	3	3	1.889e-04
GO:BP	GO:0071163	DNA replication preinitiation complex assembly	3	3	1.889e-04
GO:BP	GO:0009411	response to UV	14	155	1.910e-04
GO:BP	GO:0048513	animal organ development	104	3085	1.932e-04
GO:BP	GO:0009628	response to abiotic stimulus	49	1144	2.103e-04
GO:BP	GO:0032506	cytokinetic process	8	50	2.405e-04
GO:BP	GO:0031109	microtubule polymerization or depolymerization	13	138	2.453e-04
GO:BP	GO:0030010	establishment of cell polarity	14	159	2.510e-04
GO:BP	GO:0000132	establishment of mitotic spindle orientation	7	37	2.626e-04
GO:BP	GO:0009157	deoxyribonucleoside monophosphate biosynthetic process	4	8	2.661e-04
GO:BP	GO:1905832	positive regulation of spindle assembly	4	8	2.661e-04
GO:BP	GO:1902425	positive regulation of attachment of mitotic spindle microtubules to kinetochore	4	8	2.661e-04
GO:BP	GO:0008156	negative regulation of DNA replication	6	26	3.185e-04
GO:BP	GO:0051299	centrosome separation	5	16	3.225e-04
GO:BP	GO:0043009	chordate embryonic development	33	671	4.106e-04
GO:BP	GO:0043085	positive regulation of catalytic activity	29	554	4.146e-04
GO:BP	GO:0031399	regulation of protein modification process	45	1049	4.470e-04
GO:BP	GO:0000915	actomyosin contractile ring assembly	4	9	4.548e-04
GO:BP	GO:0000912	assembly of actomyosin apparatus involved in cytokinesis	4	9	4.548e-04
GO:BP	GO:1900264	positive regulation of DNA-directed DNA polymerase activity	4	9	4.548e-04
GO:BP	GO:1904776	regulation of protein localization to cell cortex	4	9	4.548e-04
GO:BP	GO:0062033	positive regulation of mitotic sister chromatid segregation	4	9	4.548e-04
GO:BP	GO:0042325	regulation of phosphorylation	38	830	4.764e-04
GO:BP	GO:0104004	cellular response to environmental stimulus	21	339	4.904e-04
GO:BP	GO:0071214	cellular response to abiotic stimulus	21	339	4.904e-04
GO:BP	GO:0009394	2’-deoxyribonucleotide metabolic process	7	41	5.008e-04
GO:BP	GO:0071479	cellular response to ionizing radiation	9	72	5.131e-04
GO:BP	GO:0048144	fibroblast proliferation	11	109	5.438e-04
GO:BP	GO:0051054	positive regulation of DNA metabolic process	19	291	5.629e-04
GO:BP	GO:1902531	regulation of intracellular signal transduction	71	1953	5.731e-04
GO:BP	GO:0019692	deoxyribose phosphate metabolic process	7	42	5.762e-04
GO:BP	GO:0036297	interstrand cross-link repair	7	42	5.762e-04
GO:BP	GO:0009262	deoxyribonucleotide metabolic process	7	42	5.762e-04
GO:BP	GO:0001932	regulation of protein phosphorylation	36	779	6.151e-04
GO:BP	GO:1901995	positive regulation of meiotic cell cycle phase transition	3	4	6.624e-04
GO:BP	GO:0044779	meiotic spindle checkpoint signaling	3	4	6.624e-04
GO:BP	GO:0045740	positive regulation of DNA replication	7	43	6.643e-04
GO:BP	GO:0007099	centriole replication	7	43	6.643e-04
GO:BP	GO:0044837	actomyosin contractile ring organization	4	10	6.979e-04
GO:BP	GO:0033313	meiotic cell cycle checkpoint signaling	4	10	6.979e-04
GO:BP	GO:1904668	positive regulation of ubiquitin protein ligase activity	4	10	6.979e-04
GO:BP	GO:2000104	negative regulation of DNA-templated DNA replication	4	10	6.979e-04
GO:BP	GO:0044093	positive regulation of molecular function	39	884	7.866e-04
GO:BP	GO:1902808	positive regulation of cell cycle G1/S phase transition	8	61	9.369e-04
GO:BP	GO:0033314	mitotic DNA replication checkpoint signaling	4	11	1.061e-03
GO:BP	GO:0009966	regulation of signal transduction	99	3034	1.061e-03
GO:BP	GO:0072697	protein localization to cell cortex	4	11	1.061e-03
GO:BP	GO:0007163	establishment or maintenance of cell polarity	16	234	1.255e-03
GO:BP	GO:0072331	signal transduction by p53 class mediator	13	164	1.307e-03
GO:BP	GO:0098534	centriole assembly	7	48	1.327e-03
GO:BP	GO:1902103	negative regulation of metaphase/anaphase transition of meiotic cell cycle	3	5	1.540e-03
GO:BP	GO:1905133	negative regulation of meiotic chromosome separation	3	5	1.540e-03
GO:BP	GO:1905784	regulation of anaphase-promoting complex-dependent catabolic process	3	5	1.540e-03
GO:BP	GO:0001832	blastocyst growth	5	22	1.540e-03
GO:BP	GO:0007019	microtubule depolymerization	7	50	1.706e-03
GO:BP	GO:0019220	regulation of phosphate metabolic process	40	956	1.888e-03
GO:BP	GO:0051174	regulation of phosphorus metabolic process	40	957	1.924e-03
GO:BP	GO:0006301	postreplication repair	6	36	1.928e-03
GO:BP	GO:0023051	regulation of signaling	109	3478	2.077e-03
GO:BP	GO:0010646	regulation of cell communication	109	3486	2.269e-03
GO:BP	GO:0009162	deoxyribonucleoside monophosphate metabolic process	5	24	2.329e-03
GO:BP	GO:0051438	regulation of ubiquitin-protein transferase activity	6	38	2.600e-03
GO:BP	GO:0071695	anatomical structure maturation	17	277	2.707e-03
GO:BP	GO:0046605	regulation of centrosome cycle	7	54	2.717e-03
GO:BP	GO:0048146	positive regulation of fibroblast proliferation	7	54	2.717e-03
GO:BP	GO:0031145	anaphase-promoting complex-dependent catabolic process	5	25	2.816e-03
GO:BP	GO:1902102	regulation of metaphase/anaphase transition of meiotic cell cycle	3	6	2.832e-03
GO:BP	GO:0090166	Golgi disassembly	3	6	2.832e-03
GO:BP	GO:0006335	DNA replication-dependent chromatin assembly	3	6	2.832e-03
GO:BP	GO:0090402	oncogene-induced cell senescence	3	6	2.832e-03
GO:BP	GO:2000105	positive regulation of DNA-templated DNA replication	4	14	2.832e-03
GO:BP	GO:1905132	regulation of meiotic chromosome separation	3	6	2.832e-03
GO:BP	GO:0016321	female meiosis chromosome segregation	3	6	2.832e-03
GO:BP	GO:0046073	dTMP metabolic process	3	6	2.832e-03
GO:BP	GO:0007100	mitotic centrosome separation	4	14	2.832e-03
GO:BP	GO:0009221	pyrimidine deoxyribonucleotide biosynthetic process	3	6	2.832e-03
GO:BP	GO:0042148	DNA strand invasion	3	6	2.832e-03
GO:BP	GO:2000780	negative regulation of double-strand break repair	6	39	2.879e-03
GO:BP	GO:0019985	translesion synthesis	5	26	3.298e-03
GO:BP	GO:0009130	pyrimidine nucleoside monophosphate biosynthetic process	4	15	3.707e-03
GO:BP	GO:0045738	negative regulation of DNA repair	6	41	3.788e-03
GO:BP	GO:0048608	reproductive structure development	18	314	3.883e-03
GO:BP	GO:0080090	regulation of primary metabolic process	155	5390	3.895e-03
GO:BP	GO:0072698	protein localization to microtubule cytoskeleton	7	58	4.046e-03
GO:BP	GO:0061458	reproductive system development	18	318	4.483e-03
GO:BP	GO:0001824	blastocyst development	10	119	4.681e-03
GO:BP	GO:0003006	developmental process involved in reproduction	41	1038	4.723e-03
GO:BP	GO:0048308	organelle inheritance	4	16	4.736e-03
GO:BP	GO:0048313	Golgi inheritance	4	16	4.736e-03
GO:BP	GO:0030154	cell differentiation	131	4437	4.753e-03
GO:BP	GO:0009124	nucleoside monophosphate biosynthetic process	6	43	4.785e-03
GO:BP	GO:0072528	pyrimidine-containing compound biosynthetic process	6	43	4.785e-03
GO:BP	GO:0048869	cellular developmental process	131	4438	4.785e-03
GO:BP	GO:2000779	regulation of double-strand break repair	11	143	5.072e-03
GO:BP	GO:0051246	regulation of protein metabolic process	64	1855	5.072e-03
GO:BP	GO:0045137	development of primary sexual characteristics	15	243	5.425e-03
GO:BP	GO:0090398	cellular senescence	9	101	5.763e-03
GO:BP	GO:0051641	cellular localization	111	3661	5.787e-03
GO:BP	GO:0032147	activation of protein kinase activity	7	62	5.866e-03
GO:BP	GO:0044380	protein localization to cytoskeleton	7	62	5.866e-03
GO:BP	GO:0036211	protein modification process	90	2846	5.993e-03
GO:BP	GO:1900087	positive regulation of G1/S transition of mitotic cell cycle	6	45	5.993e-03
GO:BP	GO:0001701	in utero embryonic development	21	413	5.993e-03
GO:BP	GO:0099607	lateral attachment of mitotic spindle microtubules to kinetochore	2	2	5.994e-03
GO:BP	GO:0110029	negative regulation of meiosis I	2	2	5.994e-03
GO:BP	GO:1990505	mitotic DNA replication maintenance of fidelity	2	2	5.994e-03
GO:BP	GO:1902298	cell cycle DNA replication maintenance of fidelity	2	2	5.994e-03
GO:BP	GO:0140274	repair of kinetochore microtubule attachment defect	2	2	5.994e-03
GO:BP	GO:1990426	mitotic recombination-dependent replication fork processing	2	2	5.994e-03
GO:BP	GO:0140273	repair of mitotic kinetochore microtubule attachment defect	2	2	5.994e-03
GO:BP	GO:0031619	homologous chromosome orientation in meiotic metaphase I	2	2	5.994e-03
GO:BP	GO:1905318	meiosis I spindle assembly checkpoint signaling	2	2	5.994e-03
GO:BP	GO:1905325	regulation of meiosis I spindle assembly checkpoint	2	2	5.994e-03
GO:BP	GO:0071881	adenylate cyclase-inhibiting adrenergic receptor signaling pathway	2	2	5.994e-03
GO:BP	GO:0014846	esophagus smooth muscle contraction	2	2	5.994e-03
GO:BP	GO:0006997	nucleus organization	11	147	6.065e-03
GO:BP	GO:0010569	regulation of double-strand break repair via homologous recombination	8	83	6.646e-03
GO:BP	GO:0007077	mitotic nuclear membrane disassembly	3	8	6.873e-03
GO:BP	GO:0010458	exit from mitosis	5	31	6.982e-03
GO:BP	GO:0007096	regulation of exit from mitosis	4	18	7.085e-03
GO:BP	GO:0006939	smooth muscle contraction	9	105	7.202e-03
GO:BP	GO:0009790	embryo development	43	1135	7.343e-03
GO:BP	GO:0032501	multicellular organismal process	199	7322	7.376e-03
GO:BP	GO:0045814	negative regulation of gene expression, epigenetic	13	200	7.397e-03
GO:BP	GO:0031507	heterochromatin formation	11	151	7.430e-03
GO:BP	GO:0051493	regulation of cytoskeleton organization	24	517	8.468e-03
GO:BP	GO:0006221	pyrimidine nucleotide biosynthetic process	5	33	9.168e-03
GO:BP	GO:0051642	centrosome localization	5	33	9.168e-03
GO:BP	GO:0061842	microtubule organizing center localization	5	33	9.168e-03
GO:BP	GO:0031100	animal organ regeneration	7	68	9.543e-03
GO:BP	GO:0046601	positive regulation of centriole replication	3	9	9.791e-03
GO:BP	GO:0046602	regulation of mitotic centrosome separation	3	9	9.791e-03
GO:BP	GO:0090169	regulation of spindle assembly	5	34	1.045e-02
GO:BP	GO:2000243	positive regulation of reproductive process	8	90	1.088e-02
GO:BP	GO:0034644	cellular response to UV	8	90	1.088e-02
GO:BP	GO:0042311	vasodilation	6	51	1.088e-02
GO:BP	GO:1902410	mitotic cytokinetic process	5	35	1.185e-02
GO:BP	GO:0008406	gonad development	14	238	1.196e-02
GO:BP	GO:0010332	response to gamma radiation	6	52	1.199e-02
GO:BP	GO:0007548	sex differentiation	16	294	1.234e-02
GO:BP	GO:0051443	positive regulation of ubiquitin-protein transferase activity	4	21	1.248e-02
GO:BP	GO:0021700	developmental maturation	18	352	1.260e-02
GO:BP	GO:0001556	oocyte maturation	5	36	1.332e-02
GO:BP	GO:0110025	DNA strand resection involved in replication fork processing	3	10	1.336e-02
GO:BP	GO:0016477	cell migration	53	1534	1.399e-02
GO:BP	GO:0007129	homologous chromosome pairing at meiosis	6	54	1.440e-02
GO:BP	GO:0009129	pyrimidine nucleoside monophosphate metabolic process	4	22	1.470e-02
GO:BP	GO:0007018	microtubule-based movement	22	478	1.470e-02
GO:BP	GO:2000001	regulation of DNA damage checkpoint	4	22	1.470e-02
GO:BP	GO:0009177	pyrimidine deoxyribonucleoside monophosphate biosynthetic process	2	3	1.616e-02
GO:BP	GO:0072527	pyrimidine-containing compound metabolic process	7	75	1.616e-02
GO:BP	GO:0006231	dTMP biosynthetic process	2	3	1.616e-02
GO:BP	GO:0034421	post-translational protein acetylation	2	3	1.616e-02
GO:BP	GO:0071312	cellular response to alkaloid	5	38	1.662e-02
GO:BP	GO:0071392	cellular response to estradiol stimulus	5	38	1.662e-02
GO:BP	GO:0007399	nervous system development	81	2604	1.690e-02
GO:BP	GO:0007140	male meiotic nuclear division	6	56	1.691e-02
GO:BP	GO:0009888	tissue development	66	2032	1.691e-02
GO:BP	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle	6	56	1.691e-02
GO:BP	GO:0000018	regulation of DNA recombination	10	144	1.700e-02
GO:BP	GO:0046599	regulation of centriole replication	4	23	1.700e-02
GO:BP	GO:0009219	pyrimidine deoxyribonucleotide metabolic process	4	23	1.700e-02
GO:BP	GO:0048511	rhythmic process	16	305	1.709e-02
GO:BP	GO:0009176	pyrimidine deoxyribonucleoside monophosphate metabolic process	3	11	1.709e-02
GO:BP	GO:0070601	centromeric sister chromatid cohesion	3	11	1.709e-02
GO:BP	GO:1990918	double-strand break repair involved in meiotic recombination	3	11	1.709e-02
GO:BP	GO:0009650	UV protection	3	11	1.709e-02
GO:BP	GO:0072711	cellular response to hydroxyurea	3	11	1.709e-02
GO:BP	GO:0048583	regulation of response to stimulus	116	3993	1.732e-02
GO:BP	GO:0006282	regulation of DNA repair	13	225	1.938e-02
GO:BP	GO:0006029	proteoglycan metabolic process	8	100	1.980e-02
GO:BP	GO:0009123	nucleoside monophosphate metabolic process	7	79	2.094e-02
GO:BP	GO:0006998	nuclear envelope organization	6	59	2.149e-02
GO:BP	GO:0035295	tube development	40	1101	2.154e-02
GO:BP	GO:0072710	response to hydroxyurea	3	12	2.187e-02
GO:BP	GO:0042276	error-prone translesion synthesis	3	12	2.187e-02
GO:BP	GO:0014831	gastro-intestinal system smooth muscle contraction	3	12	2.187e-02
GO:BP	GO:0051081	nuclear membrane disassembly	3	12	2.187e-02
GO:BP	GO:0071493	cellular response to UV-B	3	12	2.187e-02
GO:BP	GO:0071168	protein localization to chromatin	6	60	2.308e-02
GO:BP	GO:0008584	male gonad development	10	152	2.430e-02
GO:BP	GO:1902807	negative regulation of cell cycle G1/S phase transition	6	61	2.501e-02
GO:BP	GO:0046546	development of primary male sexual characteristics	10	153	2.538e-02
GO:BP	GO:0006760	folic acid-containing compound metabolic process	4	26	2.580e-02
GO:BP	GO:2000042	negative regulation of double-strand break repair via homologous recombination	4	26	2.580e-02
GO:BP	GO:0006915	apoptotic process	62	1923	2.625e-02
GO:BP	GO:0030866	cortical actin cytoskeleton organization	5	43	2.707e-02
GO:BP	GO:0030397	membrane disassembly	3	13	2.736e-02
GO:BP	GO:1903251	multi-ciliated epithelial cell differentiation	3	13	2.736e-02
GO:BP	GO:0031401	positive regulation of protein modification process	26	637	2.765e-02
GO:BP	GO:0008625	extrinsic apoptotic signaling pathway via death domain receptors	7	84	2.846e-02
GO:BP	GO:0009416	response to light stimulus	16	323	2.846e-02
GO:BP	GO:0046075	dTTP metabolic process	2	4	2.851e-02
GO:BP	GO:0051296	establishment of meiotic spindle orientation	2	4	2.851e-02
GO:BP	GO:1901563	response to camptothecin	2	4	2.851e-02
GO:BP	GO:0051754	meiotic sister chromatid cohesion, centromeric	2	4	2.851e-02
GO:BP	GO:1905448	positive regulation of mitochondrial ATP synthesis coupled electron transport	2	4	2.851e-02
GO:BP	GO:0009212	pyrimidine deoxyribonucleoside triphosphate biosynthetic process	2	4	2.851e-02
GO:BP	GO:0072757	cellular response to camptothecin	2	4	2.851e-02
GO:BP	GO:0007079	mitotic chromosome movement towards spindle pole	2	4	2.851e-02
GO:BP	GO:0006235	dTTP biosynthetic process	2	4	2.851e-02
GO:BP	GO:0043060	meiotic metaphase I homologous chromosome alignment	2	4	2.851e-02
GO:BP	GO:1990086	lens fiber cell apoptotic process	2	4	2.851e-02
GO:BP	GO:0009987	cellular process	467	20247	2.998e-02
GO:BP	GO:0048469	cell maturation	12	211	3.014e-02
GO:BP	GO:0045860	positive regulation of protein kinase activity	13	239	3.030e-02
GO:BP	GO:0043412	macromolecule modification	90	3030	3.185e-02
GO:BP	GO:0048870	cell motility	58	1793	3.207e-02
GO:BP	GO:0001934	positive regulation of protein phosphorylation	21	483	3.207e-02
GO:BP	GO:0051446	positive regulation of meiotic cell cycle	4	28	3.236e-02
GO:BP	GO:0051145	smooth muscle cell differentiation	6	65	3.239e-02
GO:BP	GO:0040029	epigenetic regulation of gene expression	15	299	3.239e-02
GO:BP	GO:0051177	meiotic sister chromatid cohesion	3	14	3.251e-02
GO:BP	GO:0033262	regulation of nuclear cell cycle DNA replication	3	14	3.251e-02
GO:BP	GO:0012501	programmed cell death	63	1987	3.347e-02
GO:BP	GO:0141124	intracellular signaling cassette	61	1912	3.378e-02
GO:BP	GO:0006284	base-excision repair	5	46	3.427e-02
GO:BP	GO:0008219	cell death	63	1991	3.481e-02
GO:BP	GO:0010165	response to X-ray	4	29	3.614e-02
GO:BP	GO:0070977	bone maturation	4	29	3.614e-02
GO:BP	GO:0050678	regulation of epithelial cell proliferation	17	364	3.665e-02
GO:BP	GO:0010604	positive regulation of macromolecule metabolic process	96	3288	3.684e-02
GO:BP	GO:1902117	positive regulation of organelle assembly	7	89	3.684e-02
GO:BP	GO:0035418	protein localization to synapse	7	89	3.684e-02
GO:BP	GO:0010824	regulation of centrosome duplication	5	47	3.705e-02
GO:BP	GO:0000723	telomere maintenance	10	164	3.818e-02
GO:BP	GO:0035860	glial cell-derived neurotrophic factor receptor signaling pathway	3	15	3.873e-02
GO:BP	GO:0044027	negative regulation of gene expression via chromosomal CpG island methylation	3	15	3.873e-02
GO:BP	GO:0043101	purine-containing compound salvage	3	15	3.873e-02
GO:BP	GO:0048145	regulation of fibroblast proliferation	7	90	3.873e-02
GO:BP	GO:0071772	response to BMP	10	165	3.930e-02
GO:BP	GO:0042752	regulation of circadian rhythm	8	114	3.930e-02
GO:BP	GO:0071773	cellular response to BMP stimulus	10	165	3.930e-02
GO:BP	GO:0071763	nuclear membrane organization	5	48	3.985e-02
GO:BP	GO:0051179	localization	151	5555	3.985e-02
GO:BP	GO:0044087	regulation of cellular component biogenesis	36	1011	4.290e-02
GO:BP	GO:0071962	mitotic sister chromatid cohesion, centromeric	2	5	4.297e-02
GO:BP	GO:0140499	negative regulation of mitotic spindle assembly checkpoint signaling	2	5	4.297e-02
GO:BP	GO:0001938	positive regulation of endothelial cell proliferation	7	92	4.297e-02
GO:BP	GO:0098535	de novo centriole assembly involved in multi-ciliated epithelial cell differentiation	2	5	4.297e-02
GO:BP	GO:0043137	DNA replication, removal of RNA primer	2	5	4.297e-02
GO:BP	GO:2000278	regulation of DNA biosynthetic process	7	92	4.297e-02
GO:BP	GO:0006297	nucleotide-excision repair, DNA gap filling	2	5	4.297e-02
GO:BP	GO:0051311	meiotic metaphase chromosome alignment	2	5	4.297e-02
GO:BP	GO:0031536	positive regulation of exit from mitosis	2	5	4.297e-02
GO:BP	GO:0090233	negative regulation of spindle checkpoint	2	5	4.297e-02
GO:BP	GO:0097421	liver regeneration	4	31	4.383e-02
GO:BP	GO:0009719	response to endogenous stimulus	49	1489	4.436e-02
GO:BP	GO:0090399	replicative senescence	3	16	4.507e-02
GO:BP	GO:0051782	negative regulation of cell division	3	16	4.507e-02
GO:BP	GO:0033674	positive regulation of kinase activity	13	254	4.618e-02
GO:BP	GO:0050918	positive chemotaxis	6	71	4.639e-02
GO:BP	GO:0061351	neural precursor cell proliferation	10	171	4.851e-02
GO:BP	GO:0042558	pteridine-containing compound metabolic process	4	32	4.857e-02
GO:BP	GO:2000145	regulation of cell motility	36	1022	4.892e-02
GO:BP	GO:0050673	epithelial cell proliferation	19	441	4.920e-02
GO:BP	GO:2000573	positive regulation of DNA biosynthetic process	5	51	4.921e-02
GO:BP	GO:0042327	positive regulation of phosphorylation	21	506	4.921e-02
GO:BP	GO:0045910	negative regulation of DNA recombination	5	51	4.921e-02
GO:BP	GO:0090102	cochlea development	5	51	4.921e-02
GO:BP	GO:0050767	regulation of neurogenesis	17	378	4.921e-02
KEGG	KEGG:04110	Cell cycle	47	157	1.969e-33
KEGG	KEGG:03030	DNA replication	16	36	7.231e-14
KEGG	KEGG:03460	Fanconi anemia pathway	12	54	2.356e-06
KEGG	KEGG:04114	Oocyte meiosis	17	131	7.617e-06
KEGG	KEGG:03440	Homologous recombination	10	41	7.617e-06
KEGG	KEGG:04914	Progesterone-mediated oocyte maturation	15	102	7.617e-06
KEGG	KEGG:04115	p53 signaling pathway	12	74	3.877e-05
KEGG	KEGG:04218	Cellular senescence	17	155	6.260e-05
KEGG	KEGG:04814	Motor proteins	18	193	2.823e-04
KEGG	KEGG:05166	Human T-cell leukemia virus 1 infection	17	218	4.291e-03
KEGG	KEGG:03410	Base excision repair	7	44	5.154e-03
KEGG	KEGG:03430	Mismatch repair	5	23	8.520e-03
KEGG	KEGG:00240	Pyrimidine metabolism	7	57	2.191e-02
KEGG	KEGG:05222	Small cell lung cancer	9	92	2.217e-02
KEGG	KEGG:01232	Nucleotide metabolism	8	84	4.533e-02
KEGG	KEGG:04151	PI3K-Akt signaling pathway	20	356	4.856e-02

# write.csv(table_motif2_GOKEGG_genes, "data/new/table_motif2_GOKEGG_genes.csv")

#GO:BP
table_motif2_genes_GOBP_RUV_clust <- table_motif2_GOKEGG_genes_RUV_clust %>% 
  dplyr::filter(source=="GO:BP") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

# saveRDS(table_motif2_genes_GOBP, "data/table_motif2_genes_GOBP.RDS")

table_motif2_genes_GOBP_RUV_clust %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M2 Enriched GO:BP Terms RUVs clustlike")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("GO:BP term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG Cormotif log2cpm clustlike only-5.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#KEGG
table_motif2_genes_KEGG_RUV_clust <- table_motif2_GOKEGG_genes_RUV_clust %>% 
  dplyr::filter(source=="KEGG") %>% 
  dplyr::select(p_value, term_name, intersection_size) %>% 
  dplyr::slice_min(., n=10, order_by=p_value) %>% 
  mutate(log_val = -log10(p_value))

table_motif2_genes_KEGG_RUV_clust %>% ggplot(., aes(x = log_val, y = reorder(term_name, p_value), col= intersection_size)) +
  geom_point(aes(size = intersection_size)) +
  ggtitle("M2 DEGs Enriched KEGG Terms RUVs clustlike")+
  xlab(expression("-log"[10]~"p-value"))+
  guides(col="none", size= guide_legend(title = "# of intersected \n terms"))+
  ylab("KEGG term")+
  scale_y_discrete(labels = scales::label_wrap(30))+
  theme_bw()+
  theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
        axis.title = element_text(size = 15, colour = "black"),
        axis.ticks = element_line(linewidth = 1.5),
        axis.line = element_line(linewidth = 1.5),
        axis.text = element_text(size = 10, colour = "black", angle = 0),
        strip.text = element_text(size = 15, colour = "black", face = "bold"))

Past versions of "KEGG Cormotif log2cpm clustlike only-6.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

##Attempt Cormotif with Norm Counts Only

# #now since I'm having some strange outputs with the transformed data
# #I want to try and just feed in the normalized counts only
# 
normcounts_CMF_rep <- as.data.frame(set1$normalizedCounts)
# 
#first want to cut out the replicate samples as not needed for Cormotif
normcounts_CMF <- as.data.frame(normcounts_CMF_rep) %>%
  dplyr::select(-(contains("6R")))

# #14319 genes in 36 columns, set up for plugging into Cormotif

# #now I need to set up my groupid and compid accordingly
# #put together my group id and comparison id to make the correct comparisons between experimental conditions

# #groupid tells which experimental conditions are grouped together
# #compid tells which experimental conditions should be compared against one another
# ##ie DOX24T vs DMSO24T matched control

#groupid that doesn't require changing order of matrix:
# groupid_other <- c(
#   DOX_24T_1 = 1,
#   DMSO_24T_1 = 4,
#   DOX_24R_1 = 2,
#   DMSO_24R_1 = 5,
#   DOX_144R_1 = 3,
#   DMSO_144R_1 = 6,
# 
#   DOX_24T_2 = 1,
#   DMSO_24T_2 = 4,
#   DOX_24R_2 = 2,
#   DMSO_24R_2 = 5,
#   DOX_144R_2 = 3,
#   DMSO_144R_2 = 6,
# 
#   DOX_24T_3 = 1,
#   DMSO_24T_3 = 4,
#   DOX_24R_3 = 2,
#   DMSO_24R_3 = 5,
#   DOX_144R_3 = 3,
#   DMSO_144R_3 = 6,
# 
#   DOX_24T_4 = 1,
#   DMSO_24T_4 = 4,
#   DOX_24R_4 = 2,
#   DMSO_24R_4 = 5,
#   DOX_144R_4 = 3,
#   DMSO_144R_4 = 6,
# 
#   DOX_24T_5 = 1,
#   DMSO_24T_5 = 4,
#   DOX_24R_5 = 2,
#   DMSO_24R_5 = 5,
#   DOX_144R_5 = 3,
#   DMSO_144R_5 = 6,
# 
#   DOX_24T_6 = 1,
#   DMSO_24T_6 = 4,
#   DOX_24R_6 = 2,
#   DMSO_24R_6 = 5,
#   DOX_144R_6 = 3,
#   DMSO_144R_6 = 6
# )

groupid_other <- readRDS("data/new/RUV/groupid_other_unrearranged.RDS")

compid <- data.frame(Cond1 = c(1, 3, 5), Cond2 = c(2, 4, 6))
compid1 <- data.frame(Cond1 = c(1, 2, 3), Cond2 = c(4, 5, 6))

###Run Cormotif Norm Counts Only

# #set the seed the same as the previous one to ensure consistency
# 
# #fit Cormotif model
# # set.seed(19191)
# # #only set the seed ONCE
# # 
# # motif.fit_RUV_NC_test <- cormotiffit(
# #   exprs = exprs.NC_CMF_RUV,
# #   groupid = groupid_other,
# #   compid = compid,
# #   K = 1:10,
# #   max.iter = 1000,
# #   BIC = TRUE,
# #   runtype = "counts"
# # )
# 
#saveRDS(motif.fit_RUV_NC_test, "data/new/RUV/motif.fit_RUVnormcounts_compid_250630.RDS")
motif.fit_RUV_NC_test <- readRDS("data/new/RUV/motif.fit_RUVnormcounts_250630.RDS")

###Plot Cormotif Norm Counts Only

# #plot the AIC and BIC (we're interested in the Bayesian most of all)

plotIC(motif.fit_RUV_NC_test)

Past versions of "RUVs Plot Cormotif NormCounts Only-1.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# 
# #visual check of the lowest BIC
# motif.fit_RUV_NC_test$bic
# 
# #plot the motifs
plotMotif(motif.fit_RUV_NC_test)

Past versions of "RUVs Plot Cormotif NormCounts Only-2.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

# 
#plot the probability legend
myColors <-  rev(c("#FFFFFF", "#E6E6E6" ,"#CCCCCC", "#B3B3B3", "#999999", "#808080", "#666666","#4C4C4C", "#333333", "#191919","#000000"))

plot.new()
legend('bottomleft',fill=myColors, legend =rev(c("0", "0.1", "0.2", "0.3", "0.4",  "0.5", "0.6", "0.7", "0.8","0.9", "1")), box.col="white",title = "Probability\nlegend", horiz=FALSE,title.cex=.8)

Past versions of "RUVs Plot Cormotif NormCounts Only-3.png"

Version	Author	Date
0b1ffad	emmapfort	2025-07-02

Now that I’ve finished up with Cormotif, I want to make comparisons across DEGs and Cormotif analysis to identify DEGs within my motifs I also want to find out if any of my DEGs within a certain category (DDR, DIC, p53 target genes) are enriched in a motif.

#testing for each motif whether DNA damage response genes are enriched in that motif compared to all other tested genes

DNA_damage_genes <- readRDS("data/new/RUV/DDR_genes_entrezid.RDS")

total_DNA_damage_genes <- length(DNA_damage_genes)  #Total number of DNA damage genes
#should be 65 genes

#define my Cormotif gene lists
CMF_genes <- list(
  "Motif1" = motif1_genes_matrix, "Motif2" = motif2_genes_matrix, "Motif3" = motif3_genes_matrix
)

all_tested_genes <- unique(unlist(CMF_genes))
#this has the 12087 used for clustlike+ p.post together
#usual gene set is 14319

#compute my sets
ddr_set <- unique(na.omit(DNA_damage_genes))

motif_enrichment <- purrr::map_dfr(names(CMF_genes), function(motif_name) {
  motif_genes <- unique(CMF_genes[[motif_name]])
  
  # #print results
  # print(motif_enrichment)
  
  # Count in motif 
  in_motif_ddr     <- sum(motif_genes %in% ddr_set)
  #number of genes inside the motif that are DDR
  in_motif_non_ddr <- length(motif_genes) - in_motif_ddr
  #number of genes inside motif that are NOT DDR
  
  # Count outside motif 
  other_genes <- setdiff(all_tested_genes, motif_genes)
  #checking the difference between all genes and motif genes
  out_motif_ddr     <- sum(other_genes %in% ddr_set)
  #all genes outside motif that are DDR
  out_motif_non_ddr <- length(other_genes) - out_motif_ddr
  #all genes outside the motif that are NOT DDR
  
  # Build contingency table
  contingency_ddr_cmf <- matrix(c(in_motif_ddr, in_motif_non_ddr,
                          out_motif_ddr, out_motif_non_ddr),
                        nrow = 2, byrow = TRUE)
  
  #print results to check size of contingency table
  print(contingency_ddr_cmf)
  
  # Perform fisher's exact test - sample size too small for chi-square
  fisher_test_ddr_cmf <- fisher.test(contingency_ddr_cmf)
  p_value <- fisher_test_ddr_cmf$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_DDR = in_motif_ddr,
    In_Motif_NonDDR = in_motif_non_ddr,
    Out_Motif_DDR = out_motif_ddr,
    Out_Motif_NonDDR = out_motif_non_ddr,
    Total_Genes = length(motif_genes),
    DNA_Damage_Proportion = in_motif_ddr / length(motif_genes) * 100,
    P_Value = fisher_test_ddr_cmf$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]   14 5624
[2,]   32 6417
     [,1] [,2]
[1,]   22 6196
[2,]   24 5845
     [,1]  [,2]
[1,]   10   221
[2,]   36 11820

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long <- motif_enrichment %>%
  select(Motif, In_Motif_DDR, In_Motif_NonDDR, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_DDR, In_Motif_NonDDR),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_DDR", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long$Category <- factor(motif_long$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions <- motif_long %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion of DNA Damage Genes per Cormotif Motif",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "DDR Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

Past versions of "Cormotif DDR Enrichment Proportion Barplots-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#print the proportions so I know the exact percentages and p values
print(motif_long)

# A tibble: 6 × 6
  Motif       P_Value Category Count Fraction Significant
  <chr>         <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1 0.0370       Yes         14  0.00248 "*"        
2 Motif1 0.0370       No        5624  0.998   "*"        
3 Motif2 0.659        Yes         22  0.00354 ""         
4 Motif2 0.659        No        6196  0.996   ""         
5 Motif3 0.0000000119 Yes         10  0.0433  "*"        
6 Motif3 0.0000000119 No         221  0.957   "*"        

DOX_cardiotox_genes <- readRDS("data/new/RUV/DIC_genes_entrezid.RDS")

total_DIC_genes <- length(DOX_cardiotox_genes)  #Total number of DNA damage genes
#should be 29

#define my Cormotif gene lists
CMF_genes <- list(
  "Motif1" = motif1_genes_matrix, "Motif2" = motif2_genes_matrix, "Motif3" = motif3_genes_matrix
)

all_tested_genes <- unique(unlist(CMF_genes))
#this has the 12087 used for clustlike+ p.post together
#usual gene set is 14319

#compute my sets
dic_set <- unique(na.omit(DOX_cardiotox_genes))

motif_enrichment_dic <- purrr::map_dfr(names(CMF_genes), function(motif_name) {
  motif_genes <- unique(CMF_genes[[motif_name]])
  
  # #print this result to compare
  # print(motif_enrichment_dic)
  
  # Count in motif 
  in_motif_dic     <- sum(motif_genes %in% dic_set)
  #number of genes inside the motif that are dic
  in_motif_non_dic <- length(motif_genes) - in_motif_dic
  #number of genes inside motif that are NOT dic
  
  # Count outside motif 
  other_genes <- setdiff(all_tested_genes, motif_genes)
  #checking the difference between all genes and motif genes
  out_motif_dic     <- sum(other_genes %in% dic_set)
  #all genes outside motif that are dic
  out_motif_non_dic <- length(other_genes) - out_motif_dic
  #all genes outside the motif that are NOT dic
  
  # Build contingency table
  contingency_dic_cmf <- matrix(c(in_motif_dic, in_motif_non_dic,
                          out_motif_dic, out_motif_non_dic),
                        nrow = 2, byrow = TRUE)
  #print my contingency table to check sample size 
  print(contingency_dic_cmf)
  
  # Perform fisher's exact test (sample size too small for chi-square)
  fisher_test_dic_cmf <- fisher.test(contingency_dic_cmf)
  p_value <- fisher_test_dic_cmf$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_dic = in_motif_dic,
    In_Motif_Nondic = in_motif_non_dic,
    Out_Motif_dic = out_motif_dic,
    Out_Motif_Nondic = out_motif_non_dic,
    Total_Genes = length(motif_genes),
    DNA_Damage_Proportion = in_motif_dic / length(motif_genes) * 100,
    P_Value = fisher_test_dic_cmf$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]    8 5630
[2,]   15 6434
     [,1] [,2]
[1,]   14 6204
[2,]    9 5860
     [,1]  [,2]
[1,]    1   230
[2,]   22 11834

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_dic <- motif_enrichment_dic %>%
  select(Motif, In_Motif_dic, In_Motif_Nondic, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_dic, In_Motif_Nondic),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_dic", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_dic$Category <- factor(motif_long_dic$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_dic <- motif_long_dic %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_dic, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_dic %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion of DOX Cardiotox Genes per Cormotif Motif",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "DIC Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

Past versions of "DIC Genes Cormotif Proportion Barplots-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#print this so I know the p-value and percentages
print(motif_long_dic)

# A tibble: 6 × 6
  Motif  P_Value Category Count Fraction Significant
  <chr>    <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1   0.299 Yes          8  0.00142 ""         
2 Motif1   0.299 No        5630  0.999   ""         
3 Motif2   0.409 Yes         14  0.00225 ""         
4 Motif2   0.409 No        6204  0.998   ""         
5 Motif3   0.359 Yes          1  0.00433 ""         
6 Motif3   0.359 No         230  0.996   ""         

p53_target_genes <- readRDS("data/new/RUV/p53_targetgenes_entrezid.RDS")

total_p53_genes <- length(p53_target_genes)  #Total number of p53 target genes
#should be 300

#define my Cormotif gene lists
CMF_genes <- list(
  "Motif1" = motif1_genes_matrix, "Motif2" = motif2_genes_matrix, "Motif3" = motif3_genes_matrix
)

all_tested_genes <- unique(unlist(CMF_genes))
#this has the 12087 used for clustlike+ p.post together
#usual gene set is 14319

#compute my sets
p53_set <- unique(na.omit(p53_target_genes))

motif_enrichment_p53 <- purrr::map_dfr(names(CMF_genes), function(motif_name) {
  motif_genes <- unique(CMF_genes[[motif_name]])
  
  # #print this dataset
  # print(motif_enrichment_p53)
  
  # Count in motif 
  in_motif_p53     <- sum(motif_genes %in% p53_set)
  #number of genes inside the motif that are p53
  in_motif_non_p53 <- length(motif_genes) - in_motif_p53
  #number of genes inside motif that are NOT p53
  
  # Count outside motif 
  other_genes <- setdiff(all_tested_genes, motif_genes)
  #checking the difference between all genes and motif genes
  out_motif_p53     <- sum(other_genes %in% p53_set)
  #all genes outside motif that are p53
  out_motif_non_p53 <- length(other_genes) - out_motif_p53
  #all genes outside the motif that are NOT p53
  
  # Build contingency table
  contingency_p53_cmf <- matrix(c(in_motif_p53, in_motif_non_p53,
                          out_motif_p53, out_motif_non_p53),
                        nrow = 2, byrow = TRUE)
  #print the results so I can visualize the contingency tables for my motifs
  print(contingency_p53_cmf)
  
  # Perform fishers exact test (sample size too small for chi-square)
  fisher_test_p53_cmf <- fisher.test(contingency_p53_cmf)
  p_value <- fisher_test_p53_cmf$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_p53 = in_motif_p53,
    In_Motif_Nonp53 = in_motif_non_p53,
    Out_Motif_p53 = out_motif_p53,
    Out_Motif_Nonp53 = out_motif_non_p53,
    Total_Genes = length(motif_genes),
    DNA_Damage_Proportion = in_motif_p53 / length(motif_genes) * 100,
    P_Value = fisher_test_p53_cmf$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]  122 5516
[2,]  102 6347
     [,1] [,2]
[1,]   84 6134
[2,]  140 5729
     [,1]  [,2]
[1,]   18   213
[2,]  206 11650

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_p53 <- motif_enrichment_p53 %>%
  select(Motif, In_Motif_p53, In_Motif_Nonp53, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_p53, In_Motif_Nonp53),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_p53", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_p53$Category <- factor(motif_long_p53$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_p53 <- motif_long_p53 %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_p53, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_p53 %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion of p53 Target Genes per Cormotif Motif",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "p53 Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

Warning: Removed 1 row containing missing values or values outside the scale range
(`geom_text()`).

Past versions of "Cormotif p53 Target Gene Enrichment Proportion Barplots-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

#print these data to check percentages and p-value
print(motif_long_p53)

# A tibble: 6 × 6
  Motif      P_Value Category Count Fraction Significant
  <chr>        <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1 0.0213      Yes        122   0.0216 *          
2 Motif1 0.0213      No        5516   0.978  *          
3 Motif2 0.0000262   Yes         84   0.0135 *          
4 Motif2 0.0000262   No        6134   0.986  *          
5 Motif3 0.000000285 Yes         18   0.0779 *          
6 Motif3 0.000000285 No         213   0.922  *          

##Cormotif Proportion Barplots New Motifs RUVs Corrected ###DDR Genes Proportion Barplot RUVs Cormotif

# DNA_damage_genes <- readRDS("data/new/RUV/DNA_damage_genes_symbolentrez.RDS")

DNA_damage_genes <- readRDS("data/new/RUV/DDR_genes_entrezid.RDS")

total_DNA_damage_genes <- length(DNA_damage_genes)  #Total number of DNA damage genes
#should be 65 genes

#define my Cormotif gene lists
CMF_genes_RUV <- list(
  "Motif1" = final_genes_1_RUV, 
  "Motif2" = final_genes_2_RUV
)

all_tested_genes_RUV <- unique(unlist(CMF_genes_RUV))
#this has the 12087 used for clustlike+ p.post together
#usual gene set is 14319

#compute my sets
ddr_set <- unique(na.omit(DNA_damage_genes))

motif_enrichment_RUV <- purrr::map_dfr(names(CMF_genes_RUV), function(motif_name) {
  motif_genes_RUV <- unique(CMF_genes_RUV[[motif_name]])
  
  #print these results
  # print(motif_enrichment_RUV)
  
  # Count in motif 
  in_motif_ddr_RUV     <- sum(motif_genes_RUV %in% ddr_set)
  #number of genes inside the motif that are DDR
  in_motif_non_ddr_RUV <- length(motif_genes_RUV) - in_motif_ddr_RUV
  #number of genes inside motif that are NOT DDR
  
  # Count outside motif 
  other_genes_RUV <- setdiff(all_tested_genes_RUV, motif_genes_RUV)
  #checking the difference between all genes and motif genes
  out_motif_ddr_RUV     <- sum(other_genes_RUV %in% ddr_set)
  #all genes outside motif that are DDR
  out_motif_non_ddr_RUV <- length(other_genes_RUV) - out_motif_ddr_RUV
  #all genes outside the motif that are NOT DDR
  
  # Build contingency table
  contingency_ddr_cmf_RUV <- matrix(c(in_motif_ddr_RUV, in_motif_non_ddr_RUV,
                          out_motif_ddr_RUV, out_motif_non_ddr_RUV),
                        nrow = 2, byrow = TRUE)
  
  #print the contingency table to check sample size
  print(contingency_ddr_cmf_RUV)
  
  # Perform fisher's exact test - sample size too small and unreliable for chi-square
  fisher_test_ddr_cmf_RUV <- fisher.test(contingency_ddr_cmf_RUV)
  p_value_RUV <- fisher_test_ddr_cmf_RUV$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_DDR = in_motif_ddr_RUV,
    In_Motif_NonDDR = in_motif_non_ddr_RUV,
    Out_Motif_DDR = out_motif_ddr_RUV,
    Out_Motif_NonDDR = out_motif_non_ddr_RUV,
    Total_Genes = length(motif_genes_RUV),
    DNA_Damage_Proportion = in_motif_ddr_RUV / length(motif_genes_RUV) * 100,
    P_Value = fisher_test_ddr_cmf_RUV$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]   24 7578
[2,]   16  485
     [,1] [,2]
[1,]   16  485
[2,]   24 7578

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_RUV <- motif_enrichment_RUV %>%
  select(Motif, In_Motif_DDR, In_Motif_NonDDR, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_DDR, In_Motif_NonDDR),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_DDR", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_RUV$Category <- factor(motif_long_RUV$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_RUV <- motif_long_RUV %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_RUV, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_RUV %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion DDR Genes per Motif RUVs clustlike + p.post",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "DDR Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

#print this to see p-value and percentages
print(motif_long_RUV)

# A tibble: 4 × 6
  Motif   P_Value Category Count Fraction Significant
  <chr>     <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1 5.67e-10 Yes         24  0.00316 *          
2 Motif1 5.67e-10 No        7578  0.997   *          
3 Motif2 5.67e-10 Yes         16  0.0319  *          
4 Motif2 5.67e-10 No         485  0.968   *          

###DIC Genes Cormotif RUVs

DOX_cardiotox_genes <- readRDS("data/new/RUV/DIC_genes_entrezid.RDS")

total_DIC_genes <- length(DOX_cardiotox_genes)  #Total number of DNA damage genes
#should be 29

#define my Cormotif gene lists
CMF_genes_RUV_clust <- list(
  "Motif1" = clust1_genes_RUV, "Motif2" = clust2_genes_RUV
)

all_tested_genes <- unique(unlist(CMF_genes_RUV_clust))
#this has the 14117 genes used for clustlike only
#usual gene set is 14319

#compute my sets
dic_set <- unique(na.omit(DOX_cardiotox_genes))

motif_enrichment_dic_RUV_clust <- purrr::map_dfr(names(CMF_genes_RUV_clust), function(motif_name) {
  motif_genes_dic_RUV_clust <- unique(CMF_genes_RUV_clust[[motif_name]])
  
  #print this to get a summary of results
  # print(motif_enrichment_dic_RUV_clust)
  
  # Count in motif 
  in_motif_dic_RUV_clust <- sum(motif_genes_dic_RUV_clust %in% dic_set)
  #number of genes inside the motif that are dic
  in_motif_non_dic_RUV_clust <- length(motif_genes_dic_RUV_clust) - in_motif_dic_RUV_clust
  #number of genes inside motif that are NOT dic
  
  # Count outside motif 
  other_genes_dic_RUV_clust <- setdiff(all_tested_genes, motif_genes_dic_RUV_clust)
  #checking the difference between all genes and motif genes
  out_motif_dic_RUV_clust     <- sum(other_genes_dic_RUV_clust %in% dic_set)
  #all genes outside motif that are dic
  out_motif_non_dic_RUV_clust <- length(other_genes_dic_RUV_clust) - out_motif_dic_RUV_clust
  #all genes outside the motif that are NOT dic
  
  # Build contingency table
  contingency_dic_cmf_RUV_clust <- matrix(c(in_motif_dic_RUV_clust,
                                            in_motif_non_dic_RUV_clust,
                                            out_motif_dic_RUV_clust,
                                            out_motif_non_dic_RUV_clust),
                                          nrow = 2, byrow = TRUE)
  #print
  print(contingency_dic_cmf_RUV_clust)
  
  # Perform fisher's exact test (sample size too small for chi-square)
  fisher_test_dic_cmf_RUV_clust <- fisher.test(contingency_dic_cmf_RUV_clust)
  p_value <- fisher_test_dic_cmf_RUV_clust$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_dic = in_motif_dic_RUV_clust,
    In_Motif_Nondic = in_motif_non_dic_RUV_clust,
    Out_Motif_dic = out_motif_dic_RUV_clust,
    Out_Motif_Nondic = out_motif_non_dic_RUV_clust,
    Total_Genes = length(motif_genes_dic_RUV_clust),
    DNA_Damage_Proportion = in_motif_dic_RUV_clust / length(motif_genes_dic_RUV_clust) * 100,
    P_Value = fisher_test_dic_cmf_RUV_clust$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1]  [,2]
[1,]   22 13578
[2,]    1   516
     [,1]  [,2]
[1,]    1   516
[2,]   22 13578

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_dic_RUV_clust <- motif_enrichment_dic_RUV_clust %>%
  select(Motif, In_Motif_dic, In_Motif_Nondic, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_dic, In_Motif_Nondic),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_dic", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_dic_RUV_clust$Category <- factor(motif_long_dic_RUV_clust$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_dic_RUV_clust <- motif_long_dic_RUV_clust %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_dic_RUV_clust, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_dic_RUV_clust %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion DOX Cardiotox Genes per Motif RUVs clustlike",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "DIC Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

#print these data to check p-value and percentages
print(motif_long_dic_RUV_clust)

# A tibble: 4 × 6
  Motif  P_Value Category Count Fraction Significant
  <chr>    <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1   0.576 Yes         22  0.00162 ""         
2 Motif1   0.576 No       13578  0.998   ""         
3 Motif2   0.576 Yes          1  0.00193 ""         
4 Motif2   0.576 No         516  0.998   ""         

###DIC Genes RUVs Cormotif Proportion Barplot clustlike + p.post

DOX_cardiotox_genes <- readRDS("data/new/RUV/DIC_genes_entrezid.RDS")

total_DIC_genes <- length(DOX_cardiotox_genes)  #Total number of DNA damage genes
#should be 29

#define my Cormotif gene lists
CMF_genes_RUV <- list(
  "Motif1" = final_genes_1_RUV, "Motif2" = final_genes_2_RUV
)

all_tested_genes <- unique(unlist(CMF_genes_RUV))
#this has the 12087 used for clustlike+ p.post together
#usual gene set is 14319

#compute my sets
dic_set <- unique(na.omit(DOX_cardiotox_genes))

motif_enrichment_dic_RUV <- purrr::map_dfr(names(CMF_genes_RUV), function(motif_name) {
  motif_genes_dic_RUV <- unique(CMF_genes_RUV[[motif_name]])
  
  # print(motif_enrichment_dic_RUV)
  
  # Count in motif 
  in_motif_dic_RUV <- sum(motif_genes_dic_RUV %in% dic_set)
  #number of genes inside the motif that are dic
  in_motif_non_dic_RUV <- length(motif_genes_dic_RUV) - in_motif_dic_RUV
  #number of genes inside motif that are NOT dic
  
  # Count outside motif 
  other_genes_dic_RUV <- setdiff(all_tested_genes, motif_genes_dic_RUV)
  #checking the difference between all genes and motif genes
  out_motif_dic_RUV     <- sum(other_genes_dic_RUV %in% dic_set)
  #all genes outside motif that are dic
  out_motif_non_dic_RUV <- length(other_genes_dic_RUV) - out_motif_dic_RUV
  #all genes outside the motif that are NOT dic
  
  # Build contingency table
  contingency_dic_cmf_RUV <- matrix(c(in_motif_dic_RUV, in_motif_non_dic_RUV,
                          out_motif_dic_RUV, out_motif_non_dic_RUV),
                        nrow = 2, byrow = TRUE)
  
  #print contingency table
  print(contingency_dic_cmf_RUV)
  
  # Perform fisher's exact test
  fisher_test_dic_cmf_RUV <- fisher.test(contingency_dic_cmf_RUV)
  p_value <- fisher_test_dic_cmf_RUV$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_dic = in_motif_dic_RUV,
    In_Motif_Nondic = in_motif_non_dic_RUV,
    Out_Motif_dic = out_motif_dic_RUV,
    Out_Motif_Nondic = out_motif_non_dic_RUV,
    Total_Genes = length(motif_genes_dic_RUV),
    DNA_Damage_Proportion = in_motif_dic_RUV / length(motif_genes_dic_RUV) * 100,
    P_Value = fisher_test_dic_cmf_RUV$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]   10 7592
[2,]    0  501
     [,1] [,2]
[1,]    0  501
[2,]   10 7592

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_dic_RUV <- motif_enrichment_dic_RUV %>%
  select(Motif, In_Motif_dic, In_Motif_Nondic, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_dic, In_Motif_Nondic),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_dic", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_dic_RUV$Category <- factor(motif_long_dic_RUV$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_dic_RUV <- motif_long_dic_RUV %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_dic_RUV, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_dic_RUV %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion DOX Cardiotox Genes per Motif RUVs clustlike",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "DIC Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

Past versions of "DIC Genes Proportion Barplot Cormotif RUVs clust+p.post-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

###p53 Target Genes Cormotif RUVs

p53_target_genes <- readRDS("data/new/RUV/p53_targetgenes_entrezid.RDS")

total_p53_genes <- length(p53_target_genes)  #Total number of p53 target genes
#should be 300

#define my Cormotif gene lists
CMF_genes_RUV_clust <- list(
  "Motif1" = clust1_genes_RUV, "Motif2" = clust2_genes_RUV
)

all_tested_genes_RUV_clust <- unique(unlist(CMF_genes_RUV_clust))
#this has the 14117 used for clustlike only
#usual gene set is 14319

#compute my sets
p53_set <- unique(na.omit(p53_target_genes))

motif_enrichment_p53_RUV_clust <- purrr::map_dfr(names(CMF_genes_RUV_clust), function(motif_name) {
  motif_genes_p53_RUV_clust <- unique(CMF_genes_RUV_clust[[motif_name]])
  
  # Count in motif 
  in_motif_p53_RUV_clust     <- sum(motif_genes_p53_RUV_clust %in% p53_set)
  #number of genes inside the motif that are p53
  in_motif_non_p53_RUV_clust <- length(motif_genes_p53_RUV_clust) - in_motif_p53_RUV_clust
  #number of genes inside motif that are NOT p53
  
  # Count outside motif 
  other_genes_p53_RUV_clust <- setdiff(all_tested_genes_RUV_clust, motif_genes_p53_RUV_clust)
  #checking the difference between all genes and motif genes
  out_motif_p53_RUV_clust <- sum(other_genes_p53_RUV_clust %in% p53_set)
  #all genes outside motif that are p53
  out_motif_non_p53_RUV_clust <- length(other_genes_p53_RUV_clust) - out_motif_p53_RUV_clust
  #all genes outside the motif that are NOT p53
  
  # Build contingency table
  contingency_p53_cmf_RUV_clust <- matrix(c(in_motif_p53_RUV_clust,
                                            in_motif_non_p53_RUV_clust,
                                            out_motif_p53_RUV_clust,
                                            out_motif_non_p53_RUV_clust),
                                          nrow = 2, byrow = TRUE)
  
  #print my contingency table
  print(contingency_p53_cmf_RUV_clust)
  
  # Perform fisher's exact test
  fisher_test_p53_cmf_RUV_clust <- fisher.test(contingency_p53_cmf_RUV_clust)
  p_value_RUV_clust <- fisher_test_p53_cmf_RUV_clust$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_p53 = in_motif_p53_RUV_clust,
    In_Motif_Nonp53 = in_motif_non_p53_RUV_clust,
    Out_Motif_p53 = out_motif_p53_RUV_clust,
    Out_Motif_Nonp53 = out_motif_non_p53_RUV_clust,
    Total_Genes = length(motif_genes_p53_RUV_clust),
    DNA_Damage_Proportion = in_motif_p53_RUV_clust / length(motif_genes_p53_RUV_clust) * 100,
    P_Value = fisher_test_p53_cmf_RUV_clust$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1]  [,2]
[1,]  261 13339
[2,]   29   488
     [,1]  [,2]
[1,]   29   488
[2,]  261 13339

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_p53_RUV_clust <- motif_enrichment_p53_RUV_clust %>%
  select(Motif, In_Motif_p53, In_Motif_Nonp53, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_p53, In_Motif_Nonp53),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_p53", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_p53_RUV_clust$Category <- factor(motif_long_p53_RUV_clust$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_p53_RUV_clust <- motif_long_p53_RUV_clust %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_p53_RUV_clust, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_p53_RUV_clust %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion p53 Target Genes per Motif RUVs clustlike",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "p53 Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

#print this dataframe to look at p-value and percentage
print(motif_long_p53_RUV_clust)

# A tibble: 4 × 6
  Motif      P_Value Category Count Fraction Significant
  <chr>        <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1 0.000000948 Yes        261   0.0192 *          
2 Motif1 0.000000948 No       13339   0.981  *          
3 Motif2 0.000000948 Yes         29   0.0561 *          
4 Motif2 0.000000948 No         488   0.944  *          

###p53 Target Genes Cormotif RUVs p.post + clustlike

p53_target_genes <- readRDS("data/new/RUV/p53_targetgenes_entrezid.RDS")

total_p53_genes <- length(p53_target_genes)  #Total number of p53 target genes
#should be 300

#define my Cormotif gene lists
CMF_genes_RUV <- list(
  "Motif1" = final_genes_1_RUV, 
  "Motif2" = final_genes_2_RUV
)
#7602 genes motif 1 + 501 genes motif 2

all_tested_genes_RUV <- unique(unlist(CMF_genes_RUV))
#this has the 8103 genes used for clustlike + p.post
#usual gene set is 14319

#compute my sets
p53_set <- unique(na.omit(p53_target_genes))

motif_enrichment_p53_RUV <- purrr::map_dfr(names(CMF_genes_RUV), function(motif_name) {
  motif_genes_p53_RUV <- unique(CMF_genes_RUV[[motif_name]])
  
  #print results
  # print(motif_enrichment_p53_RUV)
  
  # Count in motif 
  in_motif_p53_RUV     <- sum(motif_genes_p53_RUV %in% p53_set)
  #number of genes inside the motif that are p53
  in_motif_non_p53_RUV <- length(motif_genes_p53_RUV) - in_motif_p53_RUV
  #number of genes inside motif that are NOT p53
  
  # Count outside motif 
  other_genes_p53_RUV <- setdiff(all_tested_genes_RUV, motif_genes_p53_RUV)
  #checking the difference between all genes and motif genes
  out_motif_p53_RUV <- sum(other_genes_p53_RUV %in% p53_set)
  #all genes outside motif that are p53
  out_motif_non_p53_RUV <- length(other_genes_p53_RUV) - out_motif_p53_RUV
  #all genes outside the motif that are NOT p53
  
  # Build contingency table
  contingency_p53_cmf_RUV <- matrix(c(in_motif_p53_RUV, in_motif_non_p53_RUV,
                          out_motif_p53_RUV, out_motif_non_p53_RUV),
                        nrow = 2, byrow = TRUE)
  #print my contingency tables
  print(contingency_p53_cmf_RUV)
  
  # Perform fisher's exact test
  fisher_test_p53_cmf_RUV <- fisher.test(contingency_p53_cmf_RUV)
  p_value_RUV <- fisher_test_p53_cmf_RUV$p.value
  
  # Output summary
  tibble(
    Motif = motif_name,
    In_Motif_p53 = in_motif_p53_RUV,
    In_Motif_Nonp53 = in_motif_non_p53_RUV,
    Out_Motif_p53 = out_motif_p53_RUV,
    Out_Motif_Nonp53 = out_motif_non_p53_RUV,
    Total_Genes = length(motif_genes_p53_RUV),
    DNA_Damage_Proportion = in_motif_p53_RUV / length(motif_genes_p53_RUV) * 100,
    P_Value = fisher_test_p53_cmf_RUV$p.value
  )
}) %>%
  mutate(Significance = case_when(
    P_Value < 0.05  ~ "*",
    TRUE            ~ ""
  ))

     [,1] [,2]
[1,]  170 7432
[2,]   28  473
     [,1] [,2]
[1,]   28  473
[2,]  170 7432

# Recreate motif_long from motif_enrichment (with fixed column names)
motif_long_p53_RUV <- motif_enrichment_p53_RUV %>%
  select(Motif, In_Motif_p53, In_Motif_Nonp53, P_Value) %>%  # include P_Value
  pivot_longer(cols = c(In_Motif_p53, In_Motif_Nonp53),
               names_to = "Category", values_to = "Count") %>%
  mutate(
    Category = ifelse(Category == "In_Motif_p53", "Yes", "No"),
    Fraction = Count / ave(Count, Motif, FUN = sum),
    
    # Add significance stars inline
    Significant = case_when(
      P_Value < 0.05  ~ "*",
      TRUE            ~ ""
    )
  )

#now I want to make sure that the yes is at the top so I have to reorder
motif_long_p53_RUV$Category <- factor(motif_long_p53_RUV$Category, levels = c("Yes", "No"))

#ensure that the stars are also on top for significance
label_positions_p53_RUV <- motif_long_p53_RUV %>%
  filter(Category == "Yes") %>%
  mutate(y_pos = Fraction + 1.01)  # 101% above the bar for visual clarity

# Plot with corrected star positioning
ggplot(motif_long_p53_RUV, aes(x = Motif, y = Fraction, fill = Category)) +
  geom_bar(stat = "identity", position = "stack") +
  geom_text(
    data = label_positions_p53_RUV %>% filter(Significant != ""),
    aes(x = Motif, y = y_pos, label = Significant),
    size = 6,
    color = "black",
    fontface = "bold"
  ) +
  scale_y_continuous(labels = scales::percent_format(scale = 1), limits = c(0, 1.08)) +
  scale_fill_manual(values = c("Yes" = "#e41a1c", "No" = "#377eb8")) +
  labs(
    title = "Proportion p53 Target Genes per Motif RUVs clustlike + p.post",
    x = "Cormotif Motif",
    y = "Percentage",
    fill = "p53 Gene"
  ) +
  theme_minimal() +
  theme(
    axis.title = element_text(size = 14),
    axis.text = element_text(size = 12),
    plot.title = element_text(size = 16, hjust = 0.5)
  )

Past versions of "p53 Target Genes Cormotif RUVs p.post + clustlike-1.png"

Version	Author	Date
54b2620	emmapfort	2025-07-08

print(motif_long_p53_RUV)

# A tibble: 4 × 6
  Motif    P_Value Category Count Fraction Significant
  <chr>      <dbl> <fct>    <int>    <dbl> <chr>      
1 Motif1 0.0000332 Yes        170   0.0224 *          
2 Motif1 0.0000332 No        7432   0.978  *          
3 Motif2 0.0000332 Yes         28   0.0559 *          
4 Motif2 0.0000332 No         473   0.944  *          

Session information

sessionInfo()

R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22000)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] rstatix_0.7.2               car_3.1-3                  
 [3] carData_3.0-5               gprofiler2_0.2.3           
 [5] RUVSeq_1.40.0               EDASeq_2.40.0              
 [7] ShortRead_1.64.0            GenomicAlignments_1.42.0   
 [9] SummarizedExperiment_1.36.0 MatrixGenerics_1.18.1      
[11] matrixStats_1.5.0           Rsamtools_2.22.0           
[13] GenomicRanges_1.58.0        Biostrings_2.74.0          
[15] GenomeInfoDb_1.42.3         XVector_0.46.0             
[17] BiocParallel_1.40.0         VennDetail_1.22.0          
[19] VennDiagram_1.7.3           futile.logger_1.4.3        
[21] ggpubr_0.6.0                UpSetR_1.4.0               
[23] ggVennDiagram_1.5.2         reshape2_1.4.4             
[25] circlize_0.4.16             ComplexHeatmap_2.22.0      
[27] org.Hs.eg.db_3.20.0         AnnotationDbi_1.68.0       
[29] IRanges_2.40.0              S4Vectors_0.44.0           
[31] corrplot_0.95               ggfortify_0.4.17           
[33] ggrepel_0.9.6               biomaRt_2.62.1             
[35] scales_1.4.0                edgebundleR_0.1.4          
[37] edgeR_4.4.0                 limma_3.62.1               
[39] Biobase_2.66.0              BiocGenerics_0.52.0        
[41] lubridate_1.9.4             forcats_1.0.0              
[43] stringr_1.5.1               dplyr_1.1.4                
[45] purrr_1.0.4                 readr_2.1.5                
[47] tidyr_1.3.1                 tibble_3.2.1               
[49] ggplot2_3.5.2               tidyverse_2.0.0            
[51] workflowr_1.7.1            

loaded via a namespace (and not attached):
  [1] later_1.4.2             BiocIO_1.16.0           bitops_1.0-9           
  [4] filelock_1.0.3          R.oo_1.27.1             XML_3.99-0.18          
  [7] lifecycle_1.0.4         httr2_1.1.2             pwalign_1.2.0          
 [10] doParallel_1.0.17       rprojroot_2.0.4         MASS_7.3-61            
 [13] processx_3.8.6          lattice_0.22-6          crosstalk_1.2.1        
 [16] backports_1.5.0         magrittr_2.0.3          plotly_4.10.4          
 [19] sass_0.4.10             rmarkdown_2.29          jquerylib_0.1.4        
 [22] yaml_2.3.10             httpuv_1.6.16           DBI_1.2.3              
 [25] RColorBrewer_1.1-3      abind_1.4-8             zlibbioc_1.52.0        
 [28] R.utils_2.13.0          RCurl_1.98-1.17         rappdirs_0.3.3         
 [31] git2r_0.36.2            GenomeInfoDbData_1.2.13 svglite_2.1.3          
 [34] codetools_0.2-20        DelayedArray_0.32.0     xml2_1.3.8             
 [37] tidyselect_1.2.1        shape_1.4.6.1           UCSC.utils_1.2.0       
 [40] farver_2.1.2            BiocFileCache_2.14.0    jsonlite_2.0.0         
 [43] GetoptLong_1.0.5        Formula_1.2-5           iterators_1.0.14       
 [46] systemfonts_1.2.2       foreach_1.5.2           tools_4.4.2            
 [49] progress_1.2.3          Rcpp_1.0.14             glue_1.8.0             
 [52] gridExtra_2.3           SparseArray_1.6.0       xfun_0.52              
 [55] withr_3.0.2             formatR_1.14            fastmap_1.2.0          
 [58] latticeExtra_0.6-30     callr_3.7.6             digest_0.6.37          
 [61] timechange_0.3.0        R6_2.6.1                mime_0.13              
 [64] colorspace_2.1-1        jpeg_0.1-11             RSQLite_2.3.9          
 [67] R.methodsS3_1.8.2       utf8_1.2.5              generics_0.1.4         
 [70] data.table_1.17.0       rtracklayer_1.66.0      prettyunits_1.2.0      
 [73] httr_1.4.7              htmlwidgets_1.6.4       S4Arrays_1.6.0         
 [76] whisker_0.4.1           pkgconfig_2.0.3         gtable_0.3.6           
 [79] blob_1.2.4              hwriter_1.3.2.1         htmltools_0.5.8.1      
 [82] clue_0.3-66             kableExtra_1.4.0        png_0.1-8              
 [85] knitr_1.50              lambda.r_1.2.4          rstudioapi_0.17.1      
 [88] tzdb_0.5.0              rjson_0.2.23            curl_6.0.1             
 [91] cachem_1.1.0            GlobalOptions_0.1.2     parallel_4.4.2         
 [94] restfulr_0.0.15         pillar_1.10.2           vctrs_0.6.5            
 [97] promises_1.3.2          dbplyr_2.5.0            xtable_1.8-4           
[100] cluster_2.1.6           evaluate_1.0.3          GenomicFeatures_1.58.0 
[103] cli_3.6.3               locfit_1.5-9.12         compiler_4.4.2         
[106] futile.options_1.0.1    rlang_1.1.6             crayon_1.5.3           
[109] ggsignif_0.6.4          labeling_0.4.3          aroma.light_3.36.0     
[112] interp_1.1-6            ps_1.9.1                getPass_0.2-4          
[115] plyr_1.8.9              fs_1.6.6                stringi_1.8.7          
[118] viridisLite_0.4.2       deldir_2.0-4            lazyeval_0.2.2         
[121] Matrix_1.7-1            hms_1.1.3               bit64_4.5.2            
[124] KEGGREST_1.46.0         statmod_1.5.0           shiny_1.10.0           
[127] igraph_2.1.4            broom_1.0.8             memoise_2.0.1          
[130] bslib_0.9.0             bit_4.5.0